Systems Biology Commons^™

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

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

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 …

A Context-Forward In Vivo Functional Genomics Platform For Target Discovery And Establishing Vulnerability Context In Pancreatic Cancer, Johnathon Rose, Johnathon Lynn Rose

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a very poor patient prognosis (5-year survival of ≤ 7%). While transcriptional profiling has aided in the classification of this disease into at least two broader subtypes, this alone has so far been insufficient to inform on more nuanced patterns of oncogenic dependency. We hypothesized that a more comprehensive and granular characterization of PDAC disease diversity is required to establish relevant context for targeted therapy. To this end, we sought to establish an integrated platform to: i) more comprehensively characterize differential oncogenic signaling across our tumor models, and ii) establish …

Investigation Of Proliferation Suppressors In Genetic Fitness Screens, Walter Frank Lenoir Iv

Dissertations and Theses (Open Access)

Innovation of CRISPR gene-editing technology has provided scientists genome manipulation tools that allowed rapid advancement of scientific capabilities and thus improved our ability to systematically study mammalian genetic functional profiles. Genome-wide CRISPR knockout screens conducted in collections of human cell lines can knock out genes at multiple loci, and have provided new insights into functional roles for independent genes. This method has launched massive efforts in looking across genetic backgrounds for context specific genetic vulnerabilities within cancer. Much of the research effort thus far has been spent on optimizing phenotype distinctions between essential, genes required for cell fitness, and non-essential, …

Molecular Mechanisms Of Boron Toxicity Tolerance In Plants, Guannan Wang

LSU Doctoral Dissertations

Boron toxicity is a worldwide agricultural problem that limits crop productivity and quality. However, our understanding on the genetic responses and adaption mechanisms to boron toxicity in plants is very limited. To address this gap in our knowledge, I compared boron stress-sensitive model, Arabidopsis thaliana and its stress-adapted relative Schrenkiella parvula to study how plants respond and adapt to excess boron at physiological, genomic, transcriptomic, and metabolic levels.

The overall project goal involved integration of multi-omics datasets to develop genome to phenome interpretations. To achieve this, I developed a python package, GOMCL, to facilitate the extraction of biologically meaningful information …

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.

Wnt Signaling Determines Body Axis Polarity In Regenerating Hydra Tissue Fragments, R. Wang, R. E. Steele, Eva-Maria S. Collins

Biology Faculty Works

How an animal establishes its body axis is a fundamental question in developmental biology. The freshwater cnidarian Hydra is an attractive model for studying axis formation because it is radially symmetric, with a single oral-aboral axis. It was recently proposed that the orientation of the new body axis in a regenerating Hydra polyp is determined by the oral-aboral orientation of the actin-myosin contractile processes (myonemes) in the animal’s outer epithelial layer. However, it remained unclear how the oral-aboral polarity of the body axis would be defined. As Wnt signaling is known to control axis polarity in Hydra and bilaterians, we …

Homicide And Drug Trafficking In Impoverished Communities In Brazil, Elenice De Souza Oliveira, Braulio Figueiredo Alves Da Silva, Flavio Luiz Sapori, Gabriela Gomes Cardoso

Department of Justice Studies Faculty Scholarship and Creative Works

Many studies demonstrate that homicides are heavily concentrated in impoverished neighborhoods, but not all socially disadvantaged neighborhoods are hotbeds of violence. Conducted in Belo Horizonte, Brazil, this study hypothesizes that the association between high rates of homicide and impoverished areas is influenced by the emergence of a specific type of street drug-dealing common to favelas (slums). The study applies econometric techniques to police data on homicides and drug arrests from 2008 to 2011, as well as 2010 Census data, to test its hypothesis. The findings provide insight into the development of crime prevention policies in areas of high social vulnerability.

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 …

Preliminary Evidence Of The Role Of Medial Prefrontal Cortex In Self-Enhancement: A Transcranial Magnetic Stimulation Study, Birgitta Taylor-Lillquist, Vivek Kanpa, Maya Crawford, Mehdi El Filali, Julia Oakes, Alex Jonasz, Amanda Disney, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

Humans employ a number of strategies to improve their position in their given social hierarchy. Overclaiming involves presenting oneself as having more knowledge than one actually possesses, and it is typically invoked to increase one’s social standing. If increased expectations to possess knowledge is a perceived social pressure, such expectations should increase bouts of overclaiming. As the medial prefrontal cortex (MPFC) is sensitive to social pressure and disruption of the MPFC leads to decreases in overclaiming, we predicted that transcranial magnetic stimulation (TMS) applied to the MPFC would reduce overclaiming and the effects would be enhanced in the presence of …

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 …

Adapting Biotoxin Monitoring For The Future: An Opportunity For A Harmful Algae Bloom (Hab) Network In Casco Bay, Maine, Zachary B. Gordon

All Theses And Dissertations

Harmful Algae Blooms (HABs) related to marine biotoxins have considerable impacts on coastal communities and have been increasing in size and frequency globally. Maine is recognized as a leader in biotoxin management as it relates to bivalve shellfish, but it has been unclear how current management practices effect the growth of shellfish aquaculture and how they will adapt to future conditions. This research uses a collaborative approach to analyze the current state of biotoxin management in Maine. First, the current management practices in Maine were compared and contrasted with five other states dealing with similar issues. Then, the perspectives of …

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

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

Advancing Human Health In The Decade Ahead: Pregnancy As A Key Window For Discovery: A Burroughs Wellcome Fund Pregnancy Think Tank., Yoel Sadovsky, Sam Mesiano, Graham J Burton, Michelle Lampl, Jeffrey C Murray, Rachel M Freathy, Anita Mahadevan-Jansen, Ashley Moffett, Nathan D Price, Paul H Wise, Derek E Wildman, Ralph Snyderman, Nigel Paneth, John Anthony Capra, Marcelo A Nobrega, Yaacov Barak, Louis J Muglia

Articles, Abstracts, and Reports

Recent revolutionary advances at the intersection of medicine, omics, data sciences, computing, epidemiology, and related technologies inspire us to ponder their impact on health. Their potential impact is particularly germane to the biology of pregnancy and perinatal medicine, where limited improvement in health outcomes for women and children has remained a global challenge. We assembled a group of experts to establish a Pregnancy Think Tank to discuss a broad spectrum of major gestational disorders and adverse pregnancy outcomes that affect maternal-infant lifelong health and should serve as targets for leveraging the many recent advances. This report reflects avenues for future …

Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro

LSU Doctoral Dissertations

Cyanobacteria were the first organisms to use oxygenic photosynthesis, converting CO₂ into useful organic chemicals. However, the chemical industry has historically relied on fossil raw materials to produce organic precursors, which has contributed to global warming. Thus, cyanobacteria have emerged as sustainable stakeholders for biotechnological production. The filamentous cyanobacterium Anabaena sp. UTEX 2576 can metabolize multiple sources of Nitrogen and was studied as a platform for biotechnological production of high-value chemicals (i.e., pigments, antioxidants, vitamins and secondary metabolites). From a Chemical engineering perspective, the biomass generation in this organism was thoroughly studied by interpreting the cell as a microbial …

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 …

Coping With Stress: The Caulobacter Approach, Bronson R. Weston, Yang Cao, John J. Tyson

Biology and Medicine Through Mathematics Conference

No abstract provided.

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.

The Critical Role Of Tnf Receptors Versus Nadph Oxidase In Controlling Babesia Microti Infection, Amal Balahmar

NYMC Student Theses and Dissertations

Babesia microti is an apicomplexan parasite transmitted by tick bite that infects red blood cells. It is increasingly associated with transfusion-transmitted infections including fatal infection as the parasite survives blood banking procedures. The infection can range from asymptomatic to fatal. The parasite can persist in relatively asymptomatic individuals for up to two years. The host and parasite determinants of severity of infection and/or parasite clearance remain largely unknown. However, asplenic and immune suppressed individuals including the very young and relatively old, greater than 50 years of age, are more vulnerable to severe disease. The goal of the current research is …

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 …

Micom: Metagenome-Scale Modeling To Infer Metabolic Interactions In The Gut Microbiota., Christian Diener, Sean M Gibbons, Osbaldo Resendis-Antonio

Articles, Abstracts, and Reports

Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn's disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort of …

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 …

Computational Analysis Of Oxidative Stress In Endothelial Dysfunction: Insights On The Role Of Tetrahydrobiopterin, Ascorbate And Glutathione, Sheetal Kedar Panday

Wayne State University Dissertations

Oxidative stress and endothelial dysfunction are reported in the cardiovascular and neurovascular diseases. Oxidative stress is caused due to an increase in the generation of reactive oxygen (ROS) and nitrogen species (RNS) and incapacity of antioxidant systems to eliminate ROS and RNS. Endothelial dysfunction is characterized by a reduction in nitric oxide (NO) bioavailability. NO is constitutively produced by enzyme endothelial nitric oxide synthase (eNOS). A reduction in tetrahydrobiopterin (BH4), which is an essential cofactor of eNOS, can lead to eNOS uncoupling. There is complex interplay between the ROS/RNS and antioxidant system underlying pathophysiologies of vascular diseases, however our quantitative …

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 …

Biogeographic Variation In Resistance Of The Invasive Plant, Alliaria Petiolata, To A Powdery Mildew Fungus And Effect Of Resistance On Competitive Dynamics, Don Cipollini, Sam Davisd, Deah Lieurance, Kendra Cipollini, Volker Bahn

Biological Sciences Faculty Publications

Garlic mustard is an invasive Eurasian biennial that has spread throughout the eastern United States and southern Canada. Populations of this plant vary in their susceptibility to Erysiphe cruciferarum, a causal agent of powdery mildew disease in Brassicaceous plants. We examined whether there were biogeographic patterns in the distribution of resistance in invasive North American and native European populations of this plant. We grew plants from 78 invasive and 20 native populations and screened them for powdery mildew resistance in the greenhouse. We found that populations were mostly monomorphic for either resistance or susceptibility but that some polymorphic populations …