Systems Biology Commons^™

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 …

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 …

Mental Models And Neutrosophic Cognitive Maps (Modelos Mentales Y Mapas Cognitivos Neutrosóficos), Maykel Leyva-Vazquez, Rebeca Escobar-Jara, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In this work, elements related to mental models elicitation and analysis are addressed through causal models. Issues related to the need to include indeterminacy in causal relationships through neutrophic cognitive maps are discussed. A proposal for static analysis in neutrosophic cognitive maps is presented. The following activities are included in the proposal: Calculate, measures of centrality, Classify nodes, De-neutrosification, and Ranking nodes. As future works, the incorporation of new metrics of centrality in neutrosophic cognitive maps is proposed. The inclusion of scenario analysis to the proposal is another area of future work.

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 …

Understanding Huntington's Disease Using Machine Learning Approaches, Sonali Lokhande

KGI Theses and Dissertations

Huntington’s disease (HD) is a debilitating neurodegenerative disorder with a complex pathophysiology. Despite extensive studies to study the disease, the sequence of events through which mutant Huntingtin (mHtt) protein executes its action still remains elusive. The phenotype of HD is an outcome of numerous processes initiated by the mHtt protein along with other proteins that act as either suppressors or enhancers of the effects of mHtt protein and PolyQ aggregates. Utilizing an integrative systems biology approach, I construct and analyze a Huntington’s disease integrome using human orthologs of protein interactors of wild type and mHtt protein. Analysis of this integrome …

Superresolution Imaging Identifies That Conventional Trafficking Pathways Are Not Essential For Endoplasmic Reticulum To Outer Mitochondrial Membrane Protein Transport., Kyle Salka, Shivaprasad Bhuvanendran, Kassandra Wilson, Petros Bozidis, Mansi Mehta, Kristin Rainey, Hiromi Sesaki, George H Patterson, Jyoti K. Jaiswal, Anamaris M. Colberg-Poley

Genomics and Precision Medicine Faculty Publications

Most nuclear-encoded mitochondrial proteins traffic from the cytosol to mitochondria. Some of these proteins localize at mitochondria-associated membranes (MAM), where mitochondria are closely apposed with the endoplasmic reticulum (ER). We have previously shown that the human cytomegalovirus signal-anchored protein known as viral mitochondria-localized inhibitor of apoptosis (vMIA) traffics from the ER to mitochondria and clusters at the outer mitochondrial membrane (OMM). Here, we have examined the host pathways by which vMIA traffics from the ER to mitochondria and clusters at the OMM. By disruption of phosphofurin acidic cluster sorting protein 2 (PACS-2), mitofusins (Mfn1/2), and dynamin related protein 1 (Drp1), …

24-Month Hiv-Free Survival Among Infants Born To Hiv-Positive Women Enrolled In Option B+ Program In Kigali, Rwanda: The Kabeho Study, Michelle Gill, Heather J. Hoffman, Dieudonne Ndatimana, Placidie Mugwaneza, Laura Guay, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Lifelong antiretroviral therapy (ART) provision to all pregnant HIV-positive women (“Option B+”) has been recommended by the World Health Organization since 2013, but there remain limited data on the effects of Option B+ on long-term HIV-free survival in breastfeeding HIV-exposed infants. The Kigali Antiretroviral and Breastfeeding Assessment for the Elimination of HIV (Kabeho) study enrolled HIV-positive women from the third trimester of pregnancy to 2 weeks postpartum in 14 heath facilities implementing Option B+ in Kigali, Rwanda. Mother–child pairs in the longitudinal observational cohort were followed until 24 months postpartum, with HIV diagnostic testing at 6 weeks, and 9, 18 …

A Swift Guide To Butterflies Of North America, Second Edition., Ann B. Swengel

The Prairie Naturalist

As soon as I got my hands on A Swift Guide to Butterflies of North America, I immediately checked the species account for Aphrodite Fritillary (Speyeria aphrodite). The prairie version of this species can be sufficiently different from the typically illustrated nominate subspecies such that it must be specifically explained as being distinct. This book passed my first test—describing details that were not only essential for identifying this fritillary species but also for realizing how similar its underside can be to our prairie specialty, the stunning Regal Fritillary (S. idalia).

Much of my research on butterflies occurs in grasslands. For …

Avian Diversity, Abundance, And Nest Success Among Managed Prairies And Agricultural Plots In Oklahoma And Texas, Phillip J. Leonard, Douglas R. Wood, Wayne E. Meyer

The Prairie Naturalist

Over the last 50 years, grassland birds experienced rapid declines due to habitat loss and degradation as a result of agricultural practices. Our objective was to document the diversity, abundance, and nest success of bird communities using managed prairie and agricultural plots at the Tishomingo National Wildlife Refuge (NWR) in southern Oklahoma and Hagerman NWR in northern Texas. From April 1 to July 15, 2013–2014, point count surveys, nest searches, nest monitoring, and vegetation sampling were conducted among three habitat treatments: managed prairie, unharvested wheat, and fallow agricultural plots. Species richness values for potential nesting species were higher in managed …

Severe Drought Impacts Female Pheasant Physiology In Southwest Nebraska, Jessica A. Laskowski, Gwen C. Bachman, Joseph J. Fontaine

The Prairie Naturalist

In 2012, Nebraska experienced one of the worst droughts since the 1930s, accompanied by abnormally high temperatures. We studied the impacts of the 2012 summer drought on female ring-necked pheasant (Phasianus colchicus) body condition and baseline and stress-induced corticosterone concentrations (CORT). We hypothesized that drought conditions would reduce pheasant body condition, increase chronic stress resulting in elevated baseline CORT levels, and down-regulate pheasant stress response to acute stressors, resulting in reduced stress-induced CORT concentrations. In southwestern Nebraska, we captured female pheasants in 2012 (pre-drought) and 2013 (post-drought). Pheasants had poorer body condition after the drought. Although female CORT measures were …

Energy Sprawl Solutions, Nicola Koper

The Prairie Naturalist

Energy sprawl affects all the major conservation issues of our age, from habitat loss and fragmentation to anthropogenic noise and climate change. As such, minimizing and solving its associated problems should be a key focus for conservation biologists. Kiesecker and Naugle provide an impressive and compact book that focusses on solving environmental and social problems likely to result from a transition from non- renewable to far less efficient renewable energy sources.

Energy Sprawl Solutions summarizes numerous relevant peer-reviewed academic papers, and outlines management and planning implications of each one, ultimately resolving these into fairly clear prescriptive recommendations for moving forward. …

Unique Nesting Behavior By Trumpeter Swans (Cygnus Buccinator), Heather M. Johnson, Michael Forsberg, Letitia Reichart, Mark P. Vrtiska

The Prairie Naturalist

Nesting behavior by Trumpeter swans (Cygnus buccinator) has been well documented for most populations. Both sexes cooperate in nest construction, which takes 11–35 days to complete (Hansen et al. 1971, Cooper 1979). Nests generally range from 1.5–3.6 meters in diameter and 1.5 meters in height and are typically built on solid structures such as a muskrat (Ondatra zibethicus) house or an island (Hansen et al. 1971, Cooper 1979). However, we discovered an atypical Trumpeter swan nest built of cattail (Typha angustifolia L.) located on Vaughn Lake, in Cherry County, Nebraska on 13 May 2016.

We monitored the atypical nest by …

The Considerations Given To Determining Authorship, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! Over the past year, I have been asked by prospective authors and colleagues whether The Prairie Naturalist has criteria for authorship. Given that this issue continues to arise, it is comforting to know that I am not the only one who struggles with considerations given to determining authorship. I checked the current submission guidelines and found nothing specific, which in turn motivated me to explore what other journals such as the Journal of Wildlife Management, Proceedings of the National Academy of Sciences, and Ecology recommend to prospective authors (Merrill 2015). Much to my surprise, discussions of authorship …

One More Warbler: A Life With Birds., Laura Erickson

The Prairie Naturalist

Imagine going on a Victor Emanuel Nature Tour, seated in the van next to Victor Emanuel himself. Between birding stops, this man who has seen over 6,000 species as a world-renowned conservationist and innovator in ecotourism regales you with stories. He starts with his “spark bird”: when he was eight years old, he was taken with the beauty of a pair of Northern Cardinals (Cardinalis cardinalis), and was hooked. Whenever people pile back into the van after a birding stop, he starts another story.

That’s how One More Warbler: A Life with Birds reads, as if Emanuel sat down with …

Field Discrimination Of Prairie Deer Mice And White-Footed Mice Using Morphological Characteristics, Jacob L. Berl, Kelton M. Verble, Elizabeth A. Flaherty, Robert K.S. Swihart

The Prairie Naturalist

Field discrimination of prairie deer mice (Peromyscus maniculatus bairdii) and white-footed mice (P. leucopus noveboracensis) can be difficult throughout much of the central United States where they co-occur. We live-trapped prairie deer mice and white-footed mice within forested and row-crop habitats in central Indiana and used multiplex PCR with species-specific primers to positively determine species identification. We collected a suite of commonly measured external morphological traits (body weight and lengths of ear, hindfoot, tail, and body) from each captured animal. Individuals were assigned to species based on analysis of DNA; discriminant function analysis was used to …

Development, Evaluation, And Application Of A Novel Error Correction Method For Next Generation Sequencing Data, Isaac Akogwu

Dissertations

Tremendous evolvement in sequencing technologies and the vast availability of data due to decreasing cost of Next-Generation-Sequencing (NGS) has availed scientists the opportunity to address a wide variety of evolutionary and biological issues. NGS uses massively parallel technology to accelerate the process at the expense of accuracy and read length in comparison to earlier Sanger methods. Therefore, computational limitations exist in how much analysis and information can be gleaned from the data without performing some form of error correction.

Error correction process is laborious and consumes a lot of computational resources. Despite the existence of many NGS data error correction …

Cytoplasmic Cyclin E Mediates Resistance To Aromatase Inhibitors In Breast Cancer, Iman Doostan

Dissertations and Theses (Open Access)

Almost seventy percent of patients with breast cancer have tumors that express hormone receptors and need hormonal therapy. Aromatase inhibitors (AIs) block estrogen biosynthesis and are considered as the first line hormonal therapy for ER⁺ post-menopausal patients. However, resistance to these drugs remains a major challenge in clinic and the biology of such resistance is not completely understood. Cyclin E is deregulated in breast cancer through generation of low molecular weight isoforms that renders patients to a poor survival. Herein, we show that HR+ patients with LMW-E expressing tumors show diminished early response to neo-adjuvant AIs as well as …

Notes: Range Extension Of The Virginia Opossum (Didelphis Virginiana) In North Dakota, Lisa L. Walsh, Robert Seabloom, Cody W. Thompson

The Prairie Naturalist

The Virginia opossum (Didelphis virginiana) is broadly distributed across North America from Costa Rica in the south to southern Ontario in the north and from the southern Great Plains in the west to the eastern United States. The Virginia opossum also was introduced multiple times to thePacific Coast beginning in the late 1800s and has established populations in that region. This species is a habitat generalist known to frequent wetland and hardwood habitats but also can be found in grasslands, along forest edges, and in agricultural and suburban settings throughout its range. However, the Virginia opossum is adapted …

The Prairie Naturalist: The Journal Of The Great Plains Natural Science Society

The Prairie Naturalist

TABLE OF CONTENTS

45 EDITOR’S NOTE

RESEARCH ARTICLES

48 Avian Diversity, Abundance, and Nest Success among Managed Prairies and Agricultural Plots in Oklahoma and Texas Phillip J. Leonard, Douglas R. Wood, and Wayne E. Meyer

57 Severe Drought Impacts Female Pheasant Physiology in Southwest Nebraska Jessica A. Laskowski, Gwen C. Bachman, and Joseph J. Fontaine

66 Field Discrimination of Prairie Deer Mice and White-footed Mice using Morphological Characteristics Jacob L. Berl, Kelton M. Verble, Elizabeth A. Flaherty, and Robert K. Swihart

NOTES

72 Range Extension of the Virgina Opossum (Didelphis virginiana) in North Dakota Lisa L. Walsh

76 Prairie Falcon …

Book Reviews: Raptors Of Mexico And Central America. William S. Clark And N. John Schmitt., Jack Jack Eitniear

The Prairie Naturalist

Whether a raptor is cryptically perched in the shadows or is viewed only as a silhouette soaring in the clouds below the glaring midday sun, raptor identification can be challenging. If you are observing raptors in the North Temperate Zone, several guides (e.g., Clark and Wheeler 2001 Dunne et al.2012) will aid you with such identifications, but few resources exist for visitors south of this zone. So, if you are interested in identifying the 69 species of diurnal raptors found in Mexico and Central America, the recently released Raptors of Mexico and Central America by William S. Clark and N. …