Systems Biology Commons^™

Multi-Behavioral Endpoint Testing Of An 87-Chemical Compound Library In Freshwater Planarians, S. Zhang, D. Hagstrom, P. Hayes, A. Graham, Eva-Maria S. Collins

Biology Faculty Works

There is an increased recognition in the field of toxicology of the value of medium-to-high-throughput screening methods using in vitro and alternative animal models. We have previously introduced the asexual freshwater planarian Dugesia japonica as a new alternative animal model and proposed that it is particularly well-suited for the study of developmental neurotoxicology. In this paper, we discuss how we have expanded and automated our screening methodology to allow for fast screening of multiple behavioral endpoints, developmental toxicity, and mortality. Using an 87-compound library provided by the National Toxicology Program (NTP), consisting of known and suspected neurotoxicants, including drugs, flame …

Lekking Behavior Of A Sharp-Tailed Grouse In South-Central Nebraska, Kelsey C. King, Andrew J. Caven, Keith Geluso

The Prairie Naturalist

Sharp-tailed grouse (Tympanuchus phasianellus; STGR) occur throughout much of the northern Great Plains, and historically were suspected to have ranged as far south as Kansas (Connelly et al. 1998). Sharp-tailed grouse were the dominant grouse in Nebraska 200 years ago, but early settlers and their associated agricultural practices extirpated STGR from much of their former range, including Kansas and southern Nebraska (Sisson 1976, Johnsgard 2016). During the period of initial land conversion, the greater prairie-chicken (T. cupido; GRPC) filled the void, benefiting from small plots of cropland providing winter forage, and outcompeting the STGR (Johnsgard and Wood 1968, Svedarsky et …

Age And Growth Of Cottonwood Trees Along The Missouri River, North Dakota, Jonathan M. Friedman, Fisher R. Ankney, J. Marshall Wolf

The Prairie Naturalist

The relict plains cottonwood (Populus deltoides subsp. monilifera) forest along the Missouri River between Lakes Sakakawea and Oahe includes trees as large as two meters in diameter. We cored 24 of these trees to determine their age and suitability for flow reconstruction. Because most of the trees were rotten in the center, we developed a method to estimate the date of the center ring that accounts for the increase in ring width toward the center. Estimated center ring dates were as early as 1806. Cottonwood growth at a dry site was correlated with April–August flow prior to construction of Lake …

A Short Narrative For Writing For The Prairie Naturalist, Christopher N. Jacques

The Prairie Naturalist

The abstract should be written upon completion of the paper. A well-written abstract is a single short (≤1 line/page of text), concise, and includes 1) an introductory sentence justifying why the study was conducted, 2) a statement of the principal objectives or hypotheses tested during the study, 3) a brief description of pertinent methods, 4) a summary of significant results, 5) a punchy conclusion, and 6) management implications (i.e., utility of results explaining how, when, where, and by whom data or interpretations can be applied; Krausman and Cox 2017). Keep in mind that abstracts are read more than authors than …

Spatiotemporal Distribution Of Waterfowl Disease Outbreaks In Kansas, Usa, Thomas A. Becker, Adam A. Ahlers, Shane Hesting, David A. Haukos

The Prairie Naturalist

Causes and impacts of disease outbreaks in wild bird populations are rarely studied beyond documentation of large epizootic events. In Kansas, USA, a central disease surveillance and reporting protocol currently does not exist within the Kansas Department of Wildlife, Parks and Tourism, which has led to a lack of available knowledge of disease occurrences that could be used to predict and manage future outbreaks. We compiled historic records of documented waterbird disease outbreaks in Kansas from 1967–2014 and related the frequency of outbreaks with light geese (Ross’s goose [Anser rossii]; Snow goose [A. caerulescens]) populations from 1970–2014. We found 32 …

Book Reviews: Force Of Nature: George Fell, Founder Of The Natural Areas Movement. Arthur Melville Pearson., James R. Herkert

The Prairie Naturalist

Arthur Melville Pearson’s Force of Nature is a book that tells two very interesting and intertwined stories. One is a story of how perseverance and determination can drive an individual to accomplish great things. And the other is a story of how the modern day natural areas movement came to be. Fortunately for those interested in conservation and natural areas protection, those two stories were combined in the life of George Fell (1916-1994). In Fell’s home state of Illinois, where his impact is widely known, his name is synonymous with conservation. In other places where his impact is less well …

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society Volume 50 No. 1

The Prairie Naturalist

TABLE OF CONTENTS

1 EDITOR’S NOTE

RESEARCH ARTICLES

3 Spatiotemporal Distribution of Waterfowl Disease Outbreaks in Kansas, USA Thomas A. Becker, Adam A. Ahlers, Shane Hesting, and David A. Haukos

14 Wild Turkey Occupancy in a Prairie Landscape Joshua C. Courlas and R. Scott Lutz

24 Age and Growth of Cottonwood Trees along the Missouri River, North Dakota Jonathan M. Friedman, Fisher R. Ankeny, and Marshall Wolf

NOTES

34 Hoary Bat Impaled on Barbed Wire Fence

37 Lekking Behavior of a Sharp-Tailed Grouse in South-Central Nebraska

BOOK REVIEWS

40 Force of Nature: George Fell, Founder of The Natural Areas Movement. …

Wild Turkey Occupancy In A Prairie Landscape, Joshua C. Courlas, R. Scott Lutz

The Prairie Naturalist

We investigated wild turkey (Meleagris gallopavo) distribution in prairie landscapes in North Dakota using occupancy modeling in two stages. In 2012, we extensively surveyed ecoregions across the state and in 2013, intensively surveyed the ecoregion with the highest probability of occupancy. Occupancy models from the statewide survey indicated wild turkeys were sparse in ecoregions with primarily agricultural landscapes, were found associated with wooded riparian cover, and found most frequently in the Missouri River Plateau ecoregion. In the Missouri River Plateau, our occupancy models identified that an additive model including mean patch area of cropland fields and spatial aggregation of forest …

Generation Of Nonlinear-Differential-Equations System From A Model Of Boolean Relationships In Arabidopsis Salt Stress Network, Renee Dale

Biology and Medicine Through Mathematics Conference

No abstract provided.

Transcriptional Profiling Reveals Extraordinary Diversity Among Skeletal Muscle Tissues, Erin E. Terry, Xiping Zhang, Christy Hoffmann, Laura D. Hughes, Scott A. Lewis, Jiajia Li, Matthew J. Wallace, Lance A. Riley, Collin M. Douglas, Miguel A. Gutierrez-Monreal, Nicholas F. Lahens, Ming C. Gong, Francisco H. Andrade, Karyn A. Esser, Michael E. Hughes

Physiology Faculty Publications

Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively affect certain muscle groups. These observations suggest that factors intrinsic to muscle tissues influence their resistance to disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq to profile mRNA expression in skeletal, smooth, and cardiac muscle tissues from mice and rats. Our data set, MuscleDB, reveals extensive transcriptional diversity, with greater than 50% of transcripts differentially expressed among skeletal muscle tissues. We detect …

Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender

Student Theses 2015-Present

This paper aims to shed light on the dissonance caused by the superimposition of Dominant Human Systems on Natural Systems. I highlight the synthetic nature of Dominant Human Systems as egoic and linguistic phenomenon manufactured by a mere portion of the human population, which renders them inherently oppressive unto peoples and landscapes whose wisdom were barred from the design process. In pursuing a radical pragmatic approach to mending the simultaneous oppression and destruction of the human being and the earth, I highlight the necessity of minimizing entropic chaos caused by excess energy expenditure, an essential feature of systems that aim …

Studying Planarian Regeneration Aboard The International Space Station Within The Student Space Flight Experimental Program, Vista Ssep Mission 11 Team, D. Hagstrom, C. Bartee, Eva-Maria S. Collins

Biology Faculty Works

The growing possibilities of space travel are quickly moving from science fiction to reality. However, to realize the dream of long-term space travel, we must understand how these conditions affect biological and physiological processes. Planarians are master regenerators, famous for their ability to regenerate from very small parts of the original animal. Understanding how this self-repair works may inspire regenerative therapies in humans. Two studies conducted aboard the International Space Station (ISS) showed that planarian regeneration is possible in microgravity. One study reported no regenerative defects, whereas the other study reported behavioral and microbiome alterations post-space travel and found that …

Modeling And Analyzing An Optogenetic System For Photoactivatable Protein Dissociation, Anvin Thomas, James Schaff

Honors Scholar Theses

Computational modeling of cell-cell interactions can grant clues and can answer questions about an experiment, especially for observations about binding interactions and kinetics. This approach was used to investigate an interaction between a light-oxygen-voltage (LOV) domain and an engineered protein called Zdark (Zdk). The LOV domain is membrane-bound while Zdk is cytosolic. The LOV domain and Zdk bind strongly in dark (K_d 26.2 nM), and weakly upon exposure to blue light (K_d > 4 μM). Total internal reflection fluorescence (TIRF) images are acquired of Zdk, the fluorescent species bound to a mCherry tag, and the loss of fluorescence is …

Self-Organized Structures: Modeling Polistes Dominula Nest Construction With Simple Rules, Matthew Harrison

Electronic Theses and Dissertations

The self-organized nest construction behaviors of European paper wasps (Polistes dominula) show potential for adoption in artificial intelligence and robotic systems where centralized control proves challenging. However, P. dominula nest construction mechanisms are not fully understood. This research investigated how nest structures stimulate P. dominula worker action at different stages of nest construction. A novel stochastic site selection model, weighted by simple rules for cell age, height, and wall count, was implemented in a three-dimensional, step-by-step nest construction simulation. The simulation was built on top of a hexagonal coordinate system to improve precision and performance. Real and idealized …

Skeletal, Cardiac, And Respiratory Muscle Function And Histopathology In The P448lneo- Mouse Model Of Fkrp-Deficient Muscular Dystrophy., Qing Yu, Melissa Morales, Ning Li, Alexander G Fritz, Ren Ruobing, Anthony Blaeser, Ershia Francois, Qi-Long Lu, Kanneboyina Nagaraju, Christopher F Spurney

Genomics and Precision Medicine Faculty Publications

BACKGROUND: Fukutin-related protein (FKRP) mutations are the most common cause of dystroglycanopathies known to cause both limb girdle and congenital muscular dystrophy. The P448Lneo- mouse model has a knock-in mutation in the FKRP gene and develops skeletal, respiratory, and cardiac muscle disease.

METHODS: We studied the natural history of the P448Lneo- mouse model over 9 months and the effects of twice weekly treadmill running. Forelimb and hindlimb grip strength (Columbus Instruments) and overall activity (Omnitech Electronics) assessed skeletal muscle function. Echocardiography was performed using VisualSonics Vevo 770 (FujiFilm VisualSonics). Plethysmography was performed using whole body system (ADInstruments). Histological evaluations included …

Data-Driven Computational Approach To Study Bio-Molecular Interactions, Misagh Naderi

LSU Doctoral Dissertations

Proteins commonly convey their functions in coordination with other proteins, small molecules and/or other biological assemblies such as sugars, lipids, DNA or RNA. Understanding the nature of these interactions is therefore central to improving our knowledge of biological systems. This body of work is a consolidation of three different computational approaches to study bio-molecular interactions: large-scale protein-ligand modeling, fragment-based cheminformatics, and computational analysis of interactions in single proteins.

The first issue that is addressed in this study is the scarcity of atomic crystal structures of protein-drug complexes. In general, a drug molecule’s affinity for multiple protein targets may causes unsolicited …

Classification As Narrative: A Renewed Perspective On A Longstanding Topic In Ethnobiology, Denise M. Glover

All Faculty Scholarship

The present work offers a renewed perspective on natural-kind classification in the field of ethnobiology, one that focuses on analyzing higher-order classifications as a form of narrative. By examining changes in classification of materia medica in three main medical/pharmacological texts from three time periods of the Tibetan medicine tradition, we see an overarching shift in classification from a focus on medical efficacy to one on material substance and morphology, thus suggesting influence from pre-twenty-first century western, Linnaean science. The work then links this historical narrative to the complexities of classification of materia medica among contemporary doctors of Tibetan medicine in …

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 …

Herbivory And Drought Generate Short‐Term Stochasticity And Long‐Term Stability In A Savanna Understory Community, Corinna Riginos, Lauren M. Porensky, Kari E. Veblen, Truman P. Young

Wildland Resources Faculty Publications

Rainfall and herbivory are fundamental drivers of grassland plant dynamics, yet few studies have examined long‐term interactions between these factors in an experimental setting. Understanding such interactions is important, as rainfall is becoming increasingly erratic and native wild herbivores are being replaced by livestock. Livestock grazing and episodic low rainfall are thought to interact, leading to greater community change than either factor alone. We examined patterns of change and stability in herbaceous community composition through four dry periods, or droughts, over 15 years of the Kenya Long‐term Exclosure Experiment (KLEE), which consists of six different combinations of cattle, native wild …

The Mayfly Newsletter, Donna J. Giberson, Peter M. Grant

The Mayfly Newsletter

No abstract provided.

A Closer Look At The Items Within Three Measures Of Evolution Acceptance: Analysis Of The Mate, I-Sea, And Gaene As A Single Corpus Of Items, William L. Romine, Amber Todd, Emily M. Walter

Biological Sciences Faculty Publications

Background

Current direct Likert measures for evolution acceptance include the MATE, GAENE, and I-SEA. Pros and cons of each of these instruments have been debated, and yet there is a dearth of research teasing out their similarities and differences when they are used together in a single context beyond the fact that their measures tend to be highly correlated. We administered these to 452 college students in non-major biology classes at two research-intensive universities from the Midwestern and Western United States to investigate the measurement properties of the items within these instruments when combined as a single corpus.

Results

Factor …

Rest Upregulates Gremlin To Modulate Diffuse Intrinsic Pontine Glioma Vasculature, Shavali Shaik, Bridget Kennis, Shinji Maegawa, Keri Schadler, Yang Yanwen, Javad Nazarian, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive glial tumor that occurs in children. The extremely poor median and 5-year survival in children afflicted with DIPG highlights the need for novel biology-driven therapeutics. Here, we have implicated the chromatin remodeler and regulator of brain development called RE1 Silencing Transcription Factor (REST), in DIPG pathology. We show that REST protein is aberrantly elevated in at least 21% of DIPG tumors compared to normal controls. Its knockdown in DIPG cell lines diminished cell growth and decreased their tumorigenicity in mouse intracranial models. DIPGs are vascularized tumors and interestingly, REST loss in …

Evolutionary History Of Plant Hosts And Fungal Symbionts Predicts The Strength Of Mycorrhizal Mutualism, Jason D. Hoeksema, James D. Beaver, Sounak Chakraborty, V. Bala Chaudhary, Monique Gardes, Catherine A. Gehring, Miranda M. Hart, Elizabeth Ann Housworth, Wittaya Kaonongbua, John N. Klironomos, Marc J. Lajeunesse, James Meadow, Brook G. Milligan, Bridget J. Piculell, Anne Pringle, Megan A. Rúa, James Umbanhowar, Wolfgang Viechtbauer, Yen-Wen Wang, Gail W.T. Wilson, Peter C. Zee

Biological Sciences Faculty Publications

Most plants engage in symbioses with mycorrhizal fungi in soils and net consequences for plants vary widely from mutualism to parasitism. However, we lack a synthetic understanding of the evolutionary and ecological forces driving such variation for this or any other nutritional symbiosis. We used meta-analysis across 646 combinations of plants and fungi to show that evolutionary history explains substantially more variation in plant responses to mycorrhizal fungi than the ecological factors included in this study, such as nutrient fertilization and additional microbes. Evolutionary history also has a different influence on outcomes of ectomycorrhizal versus arbuscular mycorrhizal symbioses; the former …

Preliminary Understanding Of Complexities In Swimming Performance Of Common Minnow (Cyprinidae) Taxa, Crystal Nichols, Austin Smith, Stephen Huelsman, Cara Schemmel, Jason C. Doll, Stephen J. Jacquemin

Biological Sciences Faculty Publications

Understanding swimming performance of native freshwater fishes has implications for ecology, conservation, and management. In particular, this type of information has practical importance for improving the understanding of fish dispersal, occurrence, migration, and invasive potential. The objective of this study was to characterize swimming performance of 2 taxa from the comparatively understudied minnow family (Cyprinidae) and test for potential drivers as a function of total length, sex, habitat, morphology, or some combination. The study assessed Spotfin Shiner (Cyprinella spiloptera; n = 66) and Bluntnose Minnow (Pimephales notatus; n = 24) populations from an ontogenic range of male and …

Changes In Water Quality Of Grand Lake St. Marys Watershed Following Implementation Of A Distressed Watershed Rules Package, Stephen J. Jacquemin, Laura T. Johnson, Theresa A. Dirksen, Gregory J. Mcglinch

Biological Sciences Faculty Publications

Grand Lake St. Marys watershed has drawn attention over the past decade as water quality issues resulting from nutrient loading have come to the forefront of public opinion, political concern, and scientific study. The objective of this study was to assess long-term changes in water quality (nutrient and sediment concentrations) following the distressed watershed rules package instituted in 2011. Since that time, a variety of rules (e.g., winter manure ban) and best management practices (cover crops, manure storage or transfers, buffers, etc.) have been implemented. We used a general linear model to assess variation in total suspended solids, particulate phosphorus, …

Investigating Smoke Exposure And Chronic Obstructive Pulmonary Disease (Copd) With A Calibrated Agent Based Model (Abm) Of In Vitro Fibroblast Wound Healing., James A. Ratti

Theses and Dissertations

COPD is characterized by tissue inflammation and impaired remodeling that suggests fibroblast maintenance of structural homeostasis is dysregulated. Thus, we performed in vitro wound healing experiments on normal and diseased human lung fibroblasts and developed an ABM of fibroblasts closing a scratched monolayer using NetLogo to evaluate differences due to COPD or cigarette smoke condensate exposure. This ABM consists of a rule-set governing the healing response, accounting for cell migration, proliferation, death, activation and senescence rates; along with the effects of heterogeneous activation, phenotypic changes, serum deprivation and exposure to cigarette smoke condensate or bFGF. Simulations were performed to calibrate …

The Three Creeks Allotment Consolidation: Changing Western Federal Grazing Paradigms, Taylor Payne

Human–Wildlife Interactions

The federal government owns approximately 47% of all land in the western United States. In the state of Utah, about 64% of the land base is managed by the federal Bureau of Land Management (BLM) and the U.S. Forest Service (USFS). The government has historically issued permits to owners of private lands to allow the owners to graze their livestock on public lands. The permits (allotments) are generally of 10-year duration and allow for an annual season of use. In some cases, continued and repeated historical annual grazing practices may not be ideal for permit holders and their communities nor …

A Comparison Of Community Structure In Regulated And Unregulated Reaches In The Upper Eel River, California, Lara Stephanie Jansen

Cal Poly Humboldt theses and projects

Flow regulation of rivers by impoundments and diversions can reduce hydrological variability. As a result, densities of algae and benthic macroinvertebrates often increase, but many sensitive taxa are lost, causing shifts across the food web. In Northern California, dams that reduce winter peak floods can result in the primary consumer community becoming dominated by grazers that are relatively invulnerable to predation, which can reduce the amount of energy transferred up the trophic levels. The steeper slope of the spring hydrograph recession limb downstream of a dam can also greatly impact instream diversity of periphyton, invertebrates and fish. The dam and …

Apomixis, Hybridization, And Biodiversity In Ferns: Insights From Genera Phegopteris And Polystichum, Nikisha Patel

Graduate College Dissertations and Theses

Apomixis is an evolutionarily important phenomenon across plant lineages. The interaction of apomixis with hybridization and polyploidy can lead to complex patterns of reticulation, complicating efforts to reconstruct evolutionary history in groups where apomixis is common. Ferns, in particular, are rich in apomictic species, notably in centers of species diversity like East Asia. Eastern North America too is home to a number of apomictic species. We investigated the East Asian ferns in Polystichum sections Xiphopolystichum and Duropolystichum (Dryopteridaceae) in order to elucidate the evolutionary and biogeraphic history of seven apomictic species in the group: Polystichum tsus-simense, P. xiphophyllum, P. sinotsus-simense, …

Devonian Origin And Cenozoic Radiation In The Clubmosses (Lycopodiaceae), Weston Testo

Graduate College Dissertations and Theses

Together with the heterosporous lycophytes, the clubmoss family (Lycopodiaceae) is the sister lineage to all other vascular land plants. Given the family’s important position in the land-plant phylogeny, studying the evolutionary history of this group is an important step towards a better understanding of plant evolution. Despite this, little is known about the Lycopodiaceae, and a well-sampled, robust phylogeny of the group is lacking. The goal of this dissertation is to resolve the relationships among evolutionary lineages in the Lycopodiaceae and provide insight into the timing and drivers of diversification in the family.

First, to place the evolution of the …