Systems Biology Commons^™

Knowing What We Know: Leveraging Community Knowledge Through Automated Text-Mining, Justin Gardner, Jonathan Tory Toole, Hemant Kalia, Garry Spink Jr., Gordon Broderick

Advances in Clinical Medical Research and Healthcare Delivery

No abstract provided.

Biases And Blind-Spots In Genome-Wide Crispr-Cas9 Knockout Screens, Merve Dede

Dissertations and Theses (Open Access)

Adaptation of the bacterial CRISPR-Cas9 system to mammalian cells revolutionized the field of functional genomics, enabling genome-scale genetic perturbations to study essential genes, whose loss of function results in a severe fitness defect. There are two types of essential genes in a cell. Core essential genes are absolutely required for growth and proliferation in every cell type. On the other hand, context-dependent essential genes become essential in an environmental or genetic context. The concept of context-dependent gene essentiality is particularly important in cancer, since killing cancer cells selectively without harming surrounding healthy tissue remains a major challenge. The toxicity of …

Geological Problems With Microbiological Solutions: Deciphering The Authigenesis Of Calcite, Dolomite, And Native Sulfur In Salty Environments, Amanda L. Labrado

Open Access Theses & Dissertations

Microbial activity is known to impact the formation and alteration of many different rock types. For carbonate caprock (CCR), a lithology found on salt diapirs, it is generally accepted that microbial activity drives the precipitation of carbonate minerals, forming limestone and/or dolomite and native (elemental) sulfur. It appears that there are two types of CCR: 1) limestone associated with native sulfur (S0) and 2) limestone associated with dolomite. The mechanics of CCR formation are poorly understood. For example, it is unclear why native sulfur and dolomite are rarely found in the same CCR assemblage, and why either are formed at …

Mathematical Modeling Of Lung Inflammation: Macrophage Polarization And Ventilator-Induced Lung Injury With Methods For Predicting Outcome, Sarah B. Minucci

Theses and Dissertations

Lung insults, such as respiratory infections and lung injuries, can damage the pulmonary epithelium, with the most severe cases needing mechanical ventilation for effective breathing and survival. Furthermore, despite the benefits of mechanical ventilators, prolonged or misuse of ventilators may lead to ventilation-associated/ventilation-induced lung injury (VILI). Damaged epithelial cells within the alveoli trigger a local immune response. A key immune cell is the macrophage, which can differentiate into a spectrum of phenotypes ranging from pro- to anti-inflammatory. To gain a greater understanding of the mechanisms of the immune response in the lungs and possible outcomes, we developed several mathematical models …

A New Mathematical Theory For The Dynamics Of Large Tumor Populations, A Potential Mechanism For Cancer Dormancy & Recurrence And Experimental Observation Of Melanoma Progression In Zebrafish, Adeyinka A. Lesi

Dissertations and Theses

Cancer, a family of over a hundred disease varieties, results in 600,000 deaths in the U.S. alone. Yet, improvements in imaging technology to detect disease earlier, pharmaceutical developments to shrink or eliminate tumors, and modeling of biological interactions to guide treatment have prevented millions of deaths. Cancer patients with initially similar disease can experience vastly different outcomes, including sustained recovery, refractory disease or, remarkably, recurrence years after apparently successful treatment. The current understanding of such recurrences is that they depend on the random occurrence of critical mutations. Clearly, these biological changes appear to be sufficient for recurrence, but are they …

Status Reports Of The Fisheries And Aquatic Resources Of Western Australia 2020/21, S.J. Newman, B.S. Wise, K.G. Santoro, D.J. Gaughan

Status Reports of the Fisheries and Aquatic Resources

The Status Reports of the Fisheries and Aquatic Resources of Western Australia (SRFAR) provide an annual update on the state of the fish stocks and other aquatic resources of Western Australia (WA). These reports outline the most recent assessments of the cumulative risk status for each of the aquatic resources (assets) within WA’s six Bioregions using an Ecosystem Based Fisheries Management (EBFM) approach. The Departments’ risk based EBFM framework is the State government’s basis for management of all Western Australia’s aquatic resources.

Nitrogen Dynamics And Transport Along Flowpaths In A Rural Wetland-Stream Complex, Colton Kyro

Graduate Student Theses, Dissertations, & Professional Papers

Human activities have doubled the rate of nitrogen inputs onto the landscape resulting in elevated nitrogen concentrations in our streams. Anthropogenically applied nitrogen is largely transported to stream networks via groundwater movement. Groundwater discharge occurs in distinct points along a stream but whose influences can often persist far beyond that area due to insufficient biogeochemical removal of imported nitrogen potentially causing alterations in community structure and precipitating large algae blooms. To understand the factors governing nitrogen abundance in a historical polluted stream, I used a mass-balance approach to quantify groundwater-surface water interaction and the magnitude of groundwater nitrogen input and …

The Prairie Naturalist, Vol. 52, Issue 2, December 2020

The Prairie Naturalist

Comparing Native Bee Communities on Reconstructed and Remnant Prairie in Missouri • Joseph LaRose, Elisabeth B. Webb, and Deborah Finke

Patterns and Potential Causes of Changing Winter Bird Distributions in South Dakota • David L. Swanson, Reza Goljani Amipkhiz, and Mark D. Dixon

Greater prairie-chickens and sharp-tailed grouse have similarly high nest survival in the Nebraska Sandhills • Larkin A. Powell, Walter H. Schacht, Julia P. Ewalt, and Katie R. McCollum

Captive Ring-necked Pheasant Response to Very High Experimental Doses of Lead • Travis J. Runia and Alex J. Solem

Trends in a Greater Prairie Chicken Population Established by Translocation …

Estimating The Number Of Discrete Models Of Biological Networks, Brandilyn Stigler

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Modelling And In Silico Experimentation To Estimate The Quantity Of Covid-19 Infected Individuals In Tijuana, México, Karla A. Encinas, Luis N. Coria, Paul A. Valle

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected …

Prioritizing The Largest, Oldest Corals For Disease Intervention In A Coral Disease-Ravaged Area: Southeast Florida Coral Reef Ecosystem Conservation Area, Alysha Brunelle

All HCAS Student Capstones, Theses, and Dissertations

Coral diseases appear to be more devastating than ever before. When a virulent disease ravages a coral ecosystem, it can significantly change the population’s demographics and cause local extinctions. Disease intervention response during such an event is impossible at a landscape scale, therefore priorities must be considered. Saving the largest, oldest colonies of reef-building species is a good choice due to their high fecundity and ecological function. Their size, as a proxy for age, is an indicator of their resistance to previous perturbations which may indicate higher fitness. Their size also provides habitat to many organisms and wave resistance in …

The Prairie Naturalist, Vol. 52, Issue 1, June 2020

The Prairie Naturalist

EDITOR’S NOTE • Jane E. Austin, Ph.D., Editor-in-Chief

Factors Associated with Larval Freshwater Drum Annual Peak Density in a Nebraska Irrigation Reservoir • Brett T. Miller, Brian C. Peterson, Keith D. Koupal, and Casey W. Schoenbeck

Small mammal communities in grasslands at the Grand Forks Air Force Base, North Dakota, USA • Lynda R. Lafond, Elizabeth H. Rave, and Kathryn A. Yurkonis

Evaluation of Four Larval Fish Sampling Methods in a Large Midwestern River • Nathan J. Lederman, Anthony R. Sindt, Douglas J. Dieterman, John D. Krenz, and Shannon J. Fisher

Wood Frogs (Rana sylvatica) in Southwestern Roberts …

A Phosphoinositide-Based Model Of Actin Waves In Frustrated Phagocytosis, Marco A. Avila Ponce De Leon

Biology and Medicine Through Mathematics Conference

No abstract provided.

Dugesia Japonica Is The Best Suited Of Three Planarian Species For High-Throughput Toxicology Screening, Danielle Ireland, Veronica Bochenek , '22, Daniel Chaiken , '20, Christina Rabeler, Sumi Onoe , '21, Ameet Soni, Eva-Maria S. Collins

Biology Faculty Works

High-throughput screening (HTS) using new approach methods is revolutionizing toxicology. Asexual freshwater planarians are a promising invertebrate model for neurotoxicity HTS because their diverse behaviors can be used as quantitative readouts of neuronal function. Currently, three planarian species are commonly used in toxicology research: Dugesia japonica, Schmidtea mediterranea, and Girardia tigrina. However, only D. japonica has been demonstrated to be suitable for HTS. Here, we assess the two other species for HTS suitability by direct comparison with D. japonica. Through quantitative assessments of morphology and multiple behaviors, we assayed the effects of 4 common solvents (DMSO, …

Yeast Copper Proteins And Reactive Oxygen Species In Effecting Lifespan, Megan Bestwick

Post-Grant Reports

Mitochondria are essential organelles in most eukaryotic cells because of their role in metabolism and the production of ATP by the oxidative phosphorylation (OXPHOS) pathway, as well as other key cellular processes. Metal cofactors, such as copper (Cu) and iron (Fe), are incorporated into OXPHOS protein complexes of yeast located within the inner membrane of the mitochondria. Misincorporation or modulation of these available metals in mitochondrial enzymes leads to the production of reactive oxygen species (ROS). ROS are reactive molecules containing oxygen such as peroxides, superoxide, and hydroxyl radicals. Yeast are a good model for studying aging and the effect …

The Bioethical Significance Of “The Origin Of Man’S Ethical Behavior” (October 1941, Unpublished) By Ernest Everett Just And Hedwig Anna Schnetzler Just, Theodore Walker Jr.

Journal of the South Carolina Academy of Science

Abstract –

E. E. Just (1883-1941) is an acknowledged “pioneer” in cell biology, and he is perhaps the pioneer in study of egg cell fertilization. Here we discover that Just also made pioneering contributions to general biology and evolutionary bioethics.

Within Just’s published contributions to observational cell biology, there are substantial fragments of his theory of ethical behavior, a theory with roots in cell biology. In addition to such previously available fragments, Just’s fully developed theory is now available. This recently discovered unpublished book-length manuscript argues for the biological origins of ethical behavior (evolving from cells to humans, within a …

Captive Ring-Necked Pheasant Response To Very High Experimental Doses Of Lead, Travis J. Runia, Alex J. Solem

The Prairie Naturalist

Ingestion of spent lead pellets is a well-documented source of lead exposure in free-ranging birds, although the consequence of lead ingestion varies widely among avian guilds. Ring-necked pheasants (Phasianus colchicus) appear to be less susceptible to lead poisoning than other game birds. Our objectives were to determine survival, liver lead accumulation, and body mass change of 129 captive-raised pheasants in response to being gavage-fed 5, 10, 20, or 40 lead pellets. All pheasants survived the 21-day experiment. Liver-lead levels were positively correlated with the number of lead pellets retained and negatively correlated with beginning body mass. Change in percent body …

Evaluation Of Four Larval Fish Sampling Methods In A Large Midwestern River, Nathan J. Lederman, Anthony R. Sindt, Douglas J. Dieterman, John D. Krenz, Shannon J. Fisher

The Prairie Naturalist

Understanding limitations of larval fish capture gears is critical for developing appropriate sampling protocols and interpreting catch data. We evaluated genera richness, genera diversity, assemblage similarities, abundance indices (i.e., density or catch per unit effort [CPUE]), and sample size requirements between a surface slednet and glow-stick light traps used in 2014 and 2015 and a benthic slednet and light-emitting diode light (LED) traps used in 2015 in the Minnesota River. The surface slednet captured the greatest number of larval fish genera (15) while the LED light trap captured the fewest (1). Similarities of assemblages sampled was highest between surface and …

Comparing Native Bee Communities On Reconstructed And Remnant Prairie In Missouri, Joseph Larose, Elisabeth B. Webb, Deborah Finke

The Prairie Naturalist

The tallgrass prairie of North America is an imperiled ecosystem that has been the subject of considerable restoration effort and research in the past two decades. While native prairie plant species are purposely introduced during restoration, prairie invertebrates, including native bees (Anthophila), are not and must colonize from surrounding remnants. Prairie restorations may not support the same bee communities as remnant prairies because of habitat differences and dispersal limitations. We sampled native bees on reconstructed and remnant prairies in Missouri in the summers of 2016 and 2017 and compared the communities by evaluating species richness, diversity, and community composition. We …

Greater Prairie-Chickens And Sharp-Tailed Grouse Have Similarly High Nest Survival In The Nebraska Sandhills, Larkin Powell, Walter Schacht, Julia P. Ewald, Kathryn R. Mccollum

The Prairie Naturalist

The ranges of two native galliform species overlap in the Nebraska Sandhills, the largest contiguous grassland in North America. We monitored nests of greater prairie-chickens (Tympanuchus cupido) and sharp-tailed grouse (Tympanuchus phasianellus) in Cherry County, Nebraska, in 2015 and 2016. Our objectives were to 1) compare daily probability of nest survival between species, 2) evaluate vegetation structure at nests for potential effects on nest survival, 3) compare nest site topography between species, and 4) use a simple model of breeding season success to evaluate the potential for stable populations at our study sites. We captured and …

Wood Frogs (Rana Sylvatica) In Southwestern Roberts County And Western Grant County, South Dakota, Dennis R. Skadsen, Drew R. Davis

The Prairie Naturalist

Historically, only six records of Wood Frogs (Rana sylvatica) existed from South Dakota, all represented by museum specimens. A single specimen was collected from Hartford Beach on Big Stone Lake, Roberts County in 1922 (National Museum of Natural History, Smithsonian Institution [USNM] 65452) and five Wood Frogs were collected near the outlet of Blue Dog Lake, Day County in 1929 (USNM 312618– 312622; Fig. 1). After the 1920s, no other Wood Frogs were reported in South Dakota for the next six decades, and the species was presumed extirpated. Over (1923, 1943) reported the species was common in the …

Trends In A Greater Prairie Chicken Population Established By Translocation In North Dakota, Gary Huschle, John E. Toepfer

The Prairie Naturalist

In 1992, an effort was undertaken by the North Dakota Game and Fish Department (NDGFD), U.S. Fish and Wildlife Service, and North Dakota Chapter of the Wildlife Society to reestablish a viable population of greater prairie chickens (Tympanuchus cupido pinnatus; hereafter prairie chickens) in northeast North Dakota. The release area was centered on the Prairie Chicken Wildlife Management Area located 22.5 km northwest of Grand Forks, North Dakota, in the northern part of Grand Forks County. Topography consists of poorly drained, saline flats and swells separated by poorly drained swales and sloughs in the Red River Valley (Beringer 1995). Permanent …

Factors Associated With Larval Freshwater Drum Annual Peak Density In A Nebraska Irrigation Reservoir, Brett T. Miller, Brian C. Peterson, Keith D. Koupal, Casey W. Schoenebeck

The Prairie Naturalist

Freshwater drum (Aplodinotus grunniens) represent one of the most widely distributed fish species in North America. Identifying biotic and abiotic factors that influence larval freshwater drum densities can improve understanding of early life history. Our objective was to investigate correlations between annual peak density of larval freshwater drum and combinations of five variables (chlorophyll a, growing degree days [GDD], reservoir discharge, turbidity, and cladoceran density) from a longterm (2003–2017) monitoring program in a Nebraska irrigation reservoir. Twenty-eight a priori candidate models were assessed to determine the relative support of explanatory variables associated with annual peak density of larval freshwater drum …

Small Mammal Communities In Grasslands At The Grand Forks Air Force Base, North Dakota, Usa, Lynda R. Lafond, Elizabeth H. Rave, Kathryn A. Yurkonis

The Prairie Naturalist

Small mammals are important in grasslands but are often overlooked in management and reconstruction efforts. We sampled small mammals in three sites on the Grand Forks Air Force Base (GFAFB) located in central Grand Forks County, North Dakota, USA. The study sites varied in their management history and represented the three major types of grasslands (reconstructed prairie, old field, and hay field) within Grand Forks County. We captured 463 individuals of six species with Sherman live traps in summer (June, July, August) 2014 and 2015. We captured the most individuals and species (295 individuals of 5 species), including all shrews …

Patterns And Potential Causes Of Changing Winter Bird Distributions In South Dakota, David L. Swanson, Reza Goljani Amirkhiz, Mark D. Dixon

The Prairie Naturalist

Average winter temperatures in the north-central United States have been increasing since the 1970s, and this warming might influence winter distributions of birds in the region. Species potentially influenced by such winter warming include short-distance migrants for which the northern boundary of the winter range is influenced by temperature, such as hermit thrush (Catharus guttatus), yellow-rumped warbler (Setophaga coronata), and fox sparrow (Passerella iliaca). We examined winter records during 1974–2017 from a citizen-science bird observation database for South Dakota to determine recent trends in winter records for these three species. We compared their occurrence patterns with those for three benchmark …

Recent Observations Of Water Shrews In Northeastern South Dakota, Dennis Skadsen, Robert M. Timm

The Prairie Naturalist

North American water shrews in the genus Sorex are a complex of at least five species, three of which were recognized historically, Sorex alasksans, S. bendirii, and S. palustris (Hall 1981). Within what was previously considered the single, widespread northern species, S. palustris, two additional species are now recognized, S. albibarbis in the eastern US and Canada and S. navigator in the western United States and Canada (Hope et al. 2014; Nagorsen et al. 2017; Woodman 2018). The American water shrew (Sorex palustris) originally was documented in South Dakota by three females, two were collected 1876 and …

Final Thoughts As Editor-In-Chief, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! I write this editorial during a time of reflection as Editor-in-Chief of The Prairie Naturalist (TPN), and during unprecedented times as the global COVID-19 pandemic continues. In full disclosure, I do not have a particular topic for this editorial, other than to offer a few final thoughts as my time serving the Great Plains Natural Science Society and TPN.

Bats Of The Loess Hills Ecoregion Of Southeast Nebraska, Virgil Brack Jr, Dale W. Sparks, Darwin C. Brack

The Prairie Naturalist

We surveyed bats at 49 sites in the Loess Hills Ecoregion of southeastern Nebraska, along the western edge of the eastern forest biome in eastern Richardson, Nemaha, and Otoe counties. We completed this study shortly before the northern long-eared bat (Myotis septentrionalis) was listed by the United States Fish and Wildlife Service under the Endangered Species Act. The expectation of listing, along with potential presence of the endangered Indiana bat (Myotis sodalis), motivated the study. We captured 183 bats of five species: eastern red bat (Lasiurus borealis) (n = 103; 56 %), big brown …

Factors Limiting Reintroduced Plains Topminnow, Fundulus Sciadicus, Populations In Central Great Plains Streams, Joseph Thiessen, Keith D. Koupal, Casey W. Schoenebeck

The Prairie Naturalist

The plains topminnow (Fundulus sciadicus) is an endemic Great Plains stream fish that has experienced declines in geographic range and local abundance. Due to these declines, the species has been considered for federal protection and designated with conservation status in states throughout its historic range. The reasons for declines are likely similar to hypothesized factors for other endemic stream fish declines in the Great Plains. To investigate potential limiting factors a suite of 17 historic sites with reintroduced plains topminnow populations across Nebraska were evaluated for current populations and if plains topminnow were absent, additional fish were introduced. …