Systems Biology Commons^™

Transient Dynamics Of Infection Transmission In An Intensive Care Unit, Christopher Short, Matthew S. Mietchen, Eric T. Lofgren

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Creating A Molecular Map Of The Pediatric Lung, Quinlen F. Marshall

Forum Lectures

The newborn lung undergoes vast biochemical and physiological changes during adaptation from the intrauterine to the extrauterine environment. Lung morphogenesis continues from birth into early childhood, mediated by dynamic gene expression and a diversity of pulmonary cell types that exhibit remarkable heterogeneity. (Whitsett, JA. et al. Physiol. Rev, 2019). Surprisingly, few studies have solely focused on human lung development during this critical period, and many current studies of lung maturation rely on adult, murine, or diseased samples, limiting their insights and applicability to longitudinal pediatric lung development. Understanding the molecular and physiological nuances of pulmonary development has important clinical relevance, …

Mouth Function Determines The Shape Oscillation Pattern In Regenerating Hydra Tissue Spheres, R. Wang, T. Goel, K. Khazoyan, Ziad Sabry , '21, H. J. Quan, P. H. Diamond, Eva-Maria S. Collins

Biology Faculty Works

Hydra is a small freshwater polyp capable of regeneration from small tissue pieces and from aggregates of cells. During regeneration, a hollow bilayered sphere is formed that undergoes osmotically driven shape oscillations of inflation and rupture. These oscillations are necessary for successful regeneration. Eventually, the oscillating sphere breaks rotational symmetry along the future head-foot axis of the animal. Notably, the shape oscillations show an abrupt shift from large-amplitude, long-period oscillations to small-amplitude, short-period oscillations. It has been widely accepted that this shift in oscillation pattern is linked to symmetry breaking and axis formation, and current theoretical models of Hydra symmetry …

Phylogenetic Trees And Networks Can Serve As Powerful And Complementary Approaches For Analysis Of Genomic Data, Christopher Blair, Cécile Ané

Publications and Research

Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point-of-view we highlight some of the strengths and limitations …

Do Corporate Owned Adaptive Learning Platforms Perpetuate Banking Style Learning? Integrating Technology For Activism Into Transformational Sustainability Education, Tina M. Garner

Leadership for Sustainability Education Comprehensive Papers

We live in a world that tends to be controlled by corporations. The public school system should be wary of the problems that corporate control has on education. Even though public schools should not have corporate influence, the fact remains that they do, and this perpetuates Freire's banking style learning. Through time, the corporate influence in education was through educational materials such as book sales. Since the decline of the use of books and the growth of the use of technologies, corporations have followed suit through the sales of Adaptive Learning Platforms. Through leveraging the technology which students enjoy using, …

Temporal Gene Expression Of Mesenchymal Cells In The Pediatric Lung, Quinlen F. Marshall, Soumyaroop Bhattacharya, Gautam Bandyopadhyay, Ravi Misra, Thomas Mariani, Gloria Pryhuber

Chemistry Student Work

INTRODUCTION: The newborn lung undergoes vast biochemical and physiological changes during adaptation from the intrauterine to the extrauterine environment. Lung morphogenesis continues from birth into early childhood, mediated by dynamic gene expression and a diversity of pulmonary cell types (Whitsett, JA. et al. Physiol. Rev, 2019). Murine models demonstrate that pulmonary mesenchymal cells exhibit remarkable heterogeneity in function and morphology during development, however, confirmation of their role is lacking in human neonates and early childhood (Guo, M. et al. Nat. Comm, 2019). In addition, many current human genomic studies of lung maturation suffer from limited sample size, limiting …

The Mayfly Newsletter, Donna J. Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

A Framework For Characterising And Evaluating The Effectiveness Of Environmental Modelling, Serena H. Hamilton, Baihua Fu, Joseph H.A. Guillaume, Jennifer Badham, Sondoss Elsawah, Patricia Gober, Randall J. Hunt, Takuya Iwanaga, Anthony J. Jakeman, Daniel P. Ames, Allan Curtis, Mary C. Hill, Suzanne A. Pierce, Fateme Zare

Research outputs 2014 to 2021

Environmental modelling is transitioning from the traditional paradigm that focuses on the model and its quantitative performance to a more holistic paradigm that recognises successful model-based outcomes are closely tied to undertaking modelling as a social process, not just as a technical procedure. This paper redefines evaluation as a multi-dimensional and multi-perspective concept, and proposes a more complete framework for identifying and measuring the effectiveness of modelling that serves the new paradigm. Under this framework, evaluation considers a broader set of success criteria, and emphasises the importance of contextual factors in determining the relevance and outcome of the criteria. These …

Biological Pathway Involvement In Melanoma Heterogeneity And Drug-Induced Resistance, Sarah V. Pack

STAR Program Research Presentations

Tumors develop resistance to numerous drug therapies, and this remains a major obstacle in treating many types of non-surgical cancers. Melanoma provides a good model system for studying drug resistance in cancer due to its high propensity to incur resistance after a significant initial response to a drug. Genes that are highly expressed in melanoma cancer cells have been studied, but in order to further understand the collective function of these highly expressed genes we must analyze gene sets, or pathways. A single gene’s function is rarely independent of other genes, and pathway analysis takes this into account.

Our objective …

Novel Strategies On Characterizing Biologically Specific Protein-Protein Interaction Networks, Bi Zhao

USF Tampa Graduate Theses and Dissertations

The function, behavior, and environmental response of biological systems are essentially determined by the complex interaction and regulation of biomolecules inside the systems. Therefore, it is critical to characterize the inter-molecular interaction and regulation of biomolecules inside these systems. In this direction, many experimental techniques have been developed and these techniques have been used in many different model systems under various conditions. Consequently, a massive amount of data has been generated. These data cover multiple aspects of molecular interaction and regulation, such as protein-protein interaction, microRNA-RNA interaction, gene expression profiles, etc. While carrying rich information, these data may also contain …

Genetically Distinct Behavioral Modules Underlie Natural Variation In Thermal Performance Curves, Gregory W. Stegeman, Scott E. Baird, William S. Ryu, Asher D. Cutter

Biological Sciences Faculty Publications

Thermal reaction norms pervade organismal traits as stereotyped responses to temperature, a fundamental environmental input into sensory and physiological systems. Locomotory behavior represents an especially plastic read-out of animal response, with its dynamic dependence on environmental stimuli presenting a challenge for analysis and for understanding the genomic architecture of heritable variation. Here we characterize behavioral reaction norms as thermal performance curves for the nematode Caenorhabditis briggsae, using a collection of 23 wild isolate genotypes and 153 recombinant inbred lines to quantify the extent of genetic and plastic variation in locomotory behavior to temperature changes. By reducing the dimensionality of the …

Review Of A Field Guide To The Natural World Of The Twin Cities By John J. Moriarty, Photography By Siah L. St. Clair, Douglas H. Johnson, Bonnie Sample

The Prairie Naturalist

A Field Guide to the Natural World of the Twin Cities has two foci: natural areas in the Twin Cities of Minnesota and the species that live in each. The geographical scope is the seven counties that envelop Minneapolis and Saint Paul. The author describes nine major habitat types that can be found there: prairie, savanna, big woods, oak woods, wetlands (marshes and swamps), fens and bogs, lakes, rivers, and urban and suburban. It is useful to know that “big woods” are not just woods that are large in extent, but woodlands that occur in Minnesota and western Wisconsin dominated …

Factors Affecting White Bass Abundance In Two Missouri River Reservoirs, William J. Radigan, Mark J. Fincel

The Prairie Naturalist

Annual angler harvest of white bass (Morone chrysops) increased from 1985–2005 in Lake Oahe and Lake Sharpe, two mainstem Missouri River reservoirs in South Dakota. In 2006, harvest rates dropped appreciably in both reservoirs and remained low through 2015. It is hypothesized that a confirmed 2005 columnaris disease outbreak led to reduced annual angler harvest of white bass from both reservoirs. Mean annual angler harvest prior to the outbreak (1985–2005) in Lake Oahe decreased 65% and in Lake Sharpe decreased 57% post outbreak (2006–2015). To assess potential causes of sustained decreased adult white bass abundance in the reservoirs, …

Suitability Of Single-Pass Backpack Electrofishing To Estimate Fish Abundance And Describe Assemblage Structure In Prairie Streams, Morgan J. Kauth, David A. Schumann, Katie N.B. Graeb, William Wyatt Hoback

The Prairie Naturalist

Electrofishing is commonly used by fisheries professionals to assess fish assemblage structure and species abundance in streams. Accurate estimates of fish abundance and, consequently assemblage metrics, are typically generated with mark-recapture or maximum-likelihood depletion techniques, but doing so requires considerable sampling effort. Less intensive sampling approaches may be beneficial to fisheries managers, particularly in cases where frequent sampling of many streams is preferred. We used regression and Spearman rank-order correlation analyses to compare species catch rates and the assemblage metrics generated from single-pass electrofishing samples with multiple-pass depletion abundance estimates in Nebraska streams. We examined the influence of instream habitat …

The Prairie Naturalist, Volume 51, No. 1

The Prairie Naturalist

1 EDITOR’S NOTE

RESEARCH ARTICLES

3 Factors Affecting White Bass Abundance in Two Missouri River Reservoirs, William J. Radigan and Mark J. Fincel

17 Suitability of single-pass backpack electrofishing to estimate fish abundance and describe assemblage structure in prairie streams, Morgan J. Kauth, David A. Schumann, Katie N. B. Graeb, and W. Wyatt Hoback

NOTES

25 Channel Catfish Reproductive Traits in the Lower Platte River, Nebraska, USA - Mackenzie Zwiener, Jonathan Spurgeon, & Mark Pegg

30 Quantifying Signpost Usage By Captive Male White-Tailed Deer - Cassie L. Auxt, Eric S. Michel, and Jonathan A. Jenks.

33 Incidental Captures of Plains …

Incidental Captures Of Plains Spotted Skunks In Central South Dakota, Samantha Fino, Joshua D. Stafford, Aaron T. Pearse, Jonathan A. Jenks

The Prairie Naturalist

The plains spotted skunk (Spilogale putorius interrupta) had a historically broad distribution in the central United States, extending from the Mississippi River west to the Rocky Mountains. This subspecies of the eastern spotted skunk (S. putorius) has experienced population declines in recent decades possibly due to habitat loss and reduction of prey through conversion of grasslands and forests to croplands, as well as reductions in abandoned buildings, fence rows, creek bottoms, and wood piles throughout the region (Crabb 1948, Kaplan and Mead 1991, Gompper and Hackett 2005, Sasse 2017). Woody debris provides access to prey, and …

Channel Catfish Reproductive Traits In The Lower Platte River, Nebraska, Usa, Mackenzie Zwiener, Jonathan J. Spurgeon, Mark Pegg

The Prairie Naturalist

Reproductive traits including fecundity, egg diameter, and condition of freshwater fishes influence offspring survival and abundance and may provide insight regarding timing of reproduction (Winemiller and Rose 1992, Johnston and Leggett 2002). Fish size (i.e., length or weight) may influence the number of eggs produced by an individual female (i.e., fecundity; Michaletz 1998). Larger individuals may, thus, disproportionately contribute to year-classes through increased fecundity if egg and larval survival is similar or greater than those from smaller reproductive females (Gwinn et al. 2015). Likewise, maternal fish size may influence egg diameter and offspring survival, whereby larger egg diameters are associated …

Review Of Gulls Simplified: A Comparative Approach To Identification By Pete Dunne And Kevin T. Karlson, Garrett J. Macdonald

The Prairie Naturalist

The title of Pete Dunne and Kevin Karlson’s new book, Gulls Simplified, may seem like an oxymoron to many birders. Gulls are, after all, one of the most vexing groups of North American birds due to their myriad identification challenges, and many seasoned birders simply “don’t do gulls.” Indeed, Dunne, in the first line of the Introduction (page 13), writes, “Ask any bird-watcher to name the bird group that is most intimidating, and to a man, woman, and tour leader they often shout: GULLS!” The genesis of the book, and the authors’ approach to identification within, arises from the notion …

Do Metabolic Networks Follow A Power Law? A Psamm Analysis, Ryan Geib, Lubos Thoma, Ying Zhang

Senior Honors Projects

Inspired by the landmark paper “Emergence of Scaling in Random Networks” by Barabási and Albert, the field of network science has focused heavily on the power law distribution in recent years. This distribution has been used to model everything from the popularity of sites on the World Wide Web to the number of citations received on a scientific paper. The feature of this distribution is highlighted by the fact that many nodes (websites or papers) have few connections (internet links or citations) while few “hubs” are connected to many nodes. These properties lead to two very important observed effects: the …

Review Of Birds Of Prey Of The West: A Field Guide, By Brian K. Wheeler, Daniel Casey

The Prairie Naturalist

Birds of prey epitomize much of what attracts us to birding. Many are large and easy to observe, particularly in open landscapes. Their predatory nature and behavior give them an added aura of wildness; their migrations can be spectacular. And even veteran birders should enjoy the challenge of identifying the myriad of plumage variations shown by different ages, sexes, subspecies, and color morphs. With his newest effort, Birds of Prey of the West, Brian Wheeler has compiled a comprehensive and enhanced field guide with illustrations that stunningly capture that variation, combined with enough additional context to make it a valuable …

Review Of Carnivores Of The World, Second Edition, By Luke Hunter, Shannon M. Barber-Meyer

The Prairie Naturalist

Cracking open this fully revised field guide invites a new appreciation for the diversity of carnivores (members of the order Carnivora) in the world. Dig a little deeper and you’ll uncover just how little we know about so many of them. This second edition of the Carnivores of the World features 250 mammalian species—from a species so tiny it can squeeze through a wedding ring to one weighing thousands of times more, the polar bear (Ursus maritimus). Each detailed species account includes an illustration of the species (and sometimes varying forms or subspecies), information on morphological and identifying features, distribution …

Screening For Neurotoxic Potential Of 15 Flame Retardants Using Freshwater Planarians, S. Zhang, Danielle Ireland, N. S. Sipes, M. Behl, Eva-Maria S. Collins

Biology Faculty Works

Asexual freshwater planarians are an attractive invertebrate model for high-throughput neurotoxicity screening, because they possess multiple quantifiable behaviors to assess distinct neuronal functions. Planarians uniquely allow direct comparisons between developing and adult animals to distinguish developmentally selective effects from general neurotoxicity. In this study, we used our automated planarian screening platform to compare the neurotoxicity of 15 flame retardants (FRs), consisting of representative phased-out brominated (BFRs) and replacement organophosphorus FRs (OPFRs). OPFRs have emerged as a proposed safer alternative to BFRs; however, limited information is available on their health effects. We found 11 of the 15 FRs (3/6 BFRs, 7/8 …

Co2 Flux And C Balance Due To The Replacement Of Bare Soil With Agro-Ecological Service Crops In Mediterranean Environment, Emanuele Radicetti, O. Adewale Osipitan, Ali Reza Safahani Langeroodi, Sara Marinari, Roberto Mancinelli

Haskell Agricultural Laboratory (Northeast Research and Extension Center)

Intensive agriculture practices often results in decomposition of organic matter, thus causing soil CO₂ emissions. Agro-ecological service crop could be profitably cultivated to improve soil characteristics and reduce CO₂ emissions under Mediterranean environment. Two-year field trials were conducted in central Italy. The treatments were three agro-ecological service crops (hairy vetch, oat, and oilseed rape) and a no-service cover. Plant development, soil characteristics, and CO₂ emissions were measured. Oat and oilseed rape showed a rapid growth, while hairy vetch started to grow rapidly only after the cold period. Soil CO₂ emissions trend was similar among the agro-ecological …

Functional Feeding Groups Of Aquatic Macroinvertebrates On Natural And Artificial Leaves In Forested Stream Habitats In The Sebago Lake Land Reserve, Sam H. Matey, Kala Freytag Wistar

Thinking Matters Symposium Archive

We investigated preferential insect colonization of natural versus artificial leaves in forested streams to determine the impact of invertebrate-substrate associations on macroinvertebrate community composition and ecosystem nutrient cycling. We created 10 onion bags filled with natural maple leaves and 10 filled with artificial maple leaves, and placed 5 of each in two forested streams, one larger and one smaller, in the Sebago Lake Land Reserve in Standish, Maine. We identified the aquatic macroinvertebrates found on these samples after approximately one month to order-level and used Maine DEP biomonitoring data and functional feeding group taxonomies to classify macroinvertebrates by functional feeding …

Camera Trap Study Of The Mammal Communities Across An Urbanization Gradient, Caleb Durbin, Christine Brodsky

Posters

Urbanization impacts mammal communities due to habitat removal, resource abundance distribution, and the introduction of exotic species. Other studies have found that wildlife species richness is greatest at intermediate urbanization, while abundance is greatest in cities. This study was done to explore the mammal community across an urban to rural gradient in Pittsburg. Using motion-sensor camera traps, we documented small mammal pres­ence for 24 hours a day, finding patterns in mammal abundance, species richness, and community composition. Our hypothesis was that we will observe trends in mammal communities similar to other cities. Over six weeks, we placed two cameras in …

Student-Faculty Collaborative Research Grant Report, 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 …

Ecological Response Of Phytoplankton To The Oil Spills In The Oceans, Danling Tang, Jing Sun, Li Zhou, Sufen Wang, Ramesh P. Singh, Gang Pan

Mathematics, Physics, and Computer Science Faculty Articles and Research

Oil spills in oceans have substantial influence on marine ecosystems. This study investigates 21 oil spills in the world. Analyzing Chlorophyll-a (Chl-a) from Moderate Resolution Imaging Spectroradiomerer (MODIS) data after Penglai oil spills on 4 June 2011, found a bloom with peak value of Chl-a (13.66 mg m⁻³) spread over an area of 800 km² during 18–25 June 2011, and a pronounced increase in the monthly Chl-a concentration (6.40 mg m⁻³) on June 2012 in the Bohai Sea. Out of the 21 oil spills, 14 blooms were observed, while 11 …

South Dakota Aquatic Invertebrate Collection And Database, Ashlee Nilson, Nels H. Troelstrup Jr.

Oak Lake Field Station 30th Anniversary Retreat Presentations

No abstract provided.

Assessing The Prevalence Of Multidrug Resistant Salmonella Enterica From Stream Sediment And Poultry Litter In The Shenandoah Valley Of Virginia, Noah Greenman

Masters Theses, 2010-2019

Multidrug resistant Salmonella enterica present in stream sediment and poultry litter represent a critical health concern. A small number of S. enterica serotypes are responsible for most lab-confirmed infections in the US each year. To assess the prevalence of these significant strains, we isolated 88 S. enterica from stream sediment and poultry litter. Sequence data for all isolates were generated using an Illumina® sequencing platform, with long-reads for some isolates from the Oxford Nanopore MinION™ used in a hybrid genome assembly approach. Isolates were typed according to their serotype and multi-locus sequence type using SeqSero/SISTR and Enterobase respectively. Antibiotic resistance …

Determination Of Optimal Parameter Estimates For Medical Interventions In Human Metabolism And Inflammation, Marcella Torres

Theses and Dissertations

In this work we have developed three ordinary differential equation models of biological systems: body mass change in response to exercise, immune system response to a general inflammatory stimulus, and the immune system response in atherosclerosis. The purpose of developing such computational tools is to test hypotheses about the underlying biological processes that drive system outcomes as well as possible real medical interventions. Therefore, we focus our analysis on understanding key interactions between model parameters and outcomes to deepen our understanding of these complex processes as a means to developing effective treatments in obesity, sarcopenia, and inflammatory diseases.

We develop …