Systems Biology Commons^™

The Potential Of Epigenetics Research To Transform Conceptions Of Phenotype Development, David S. Moore

Pitzer Faculty Publications and Research

Epigenetics remains an exciting subdiscipline of biology, generating discoveries and insights about development. Because epigenetic phenomena can draw attention to the dynamic, interactional, and probabilistic nature of phenotype development, epigenetics research could hasten the demise of both nature-nurture debates and reductionist, genetically determinist perspectives on phenotype development. However, new data alone will not inevitably transform conceptualizations of phenotype origins, because it remains possible to assimilate epigenetic phenomena into traditional conceptual frameworks; epigenetic discoveries could even strengthen biologically determinist conclusions if traditional conceptualizations are retained. Although epigenetics will not force conceptual transformation, epigenetics research encourages the dismissal of the nature-nurture dichotomy …

Effect Of Endurance Exercise On Micrornas In Myositis Skeletal Muscle-A Randomized Controlled Study., Jessica F Boehler, Marshall W Hogarth, Matthew D Barberio, James S Novak, Svetlana Ghimbovschi, Kristy J Brown, Li Alemo Munters, Ingela Loell, Yi-Wen Chen, Heather Gordish-Dressman, Helene Alexanderson, Ingrid E Lundberg, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

Objective

To identify changes in skeletal muscle microRNA expression after endurance exercise and associate the identified microRNAs with mRNA and protein expression to disease-specific pathways in polymyositis (PM) and dermatomyositis (DM) patients.

Methods

Following a parallel clinical trial design, patients with probable PM or DM, exercising less than once a week, and on stable medication for at least one month were randomized into two groups at Karolinska University Hospital: a 12-week endurance exercise group (n = 12) or a non-exercised control group (n = 11). Using an Affymetrix microarray, microRNA expression was determined in paired muscle biopsies taken before and …

Molecular Signatures Of Differential Responses To Exercise Trainings During Rehabilitation., Yi-Wen Chen, Chris Gregory, Fan Ye, Naoe Harafuji, Donovan Lott, San-Huei Lai, Sunita Mathur, Mark Scarborough, Parker Gibbs, Celine Baligand, Krista Vandenborne

Genomics and Precision Medicine Faculty Publications

The loss and recovery of muscle mass and function following injury and during rehabilitation varies among individuals. While recent expression profiling studies have illustrated transcriptomic responses to muscle disuse and remodeling, how these changes contribute to the physiological responses are not clear. In this study, we quantified the effects of immobilization and subsequent rehabilitation training on muscle size and identified molecular pathways associated with muscle responsiveness in an orthopaedic patient cohort study. The injured leg of 16 individuals with ankle injury was immobilized for a minimum of 4 weeks, followed by a 6-week rehabilitation program. The maximal cross-sectional area (CSA) …

Evidence Of Morphological And Functional Variation Among Bluegill Lepomis Macrochirus Populations Across Grand Lake St Mary's Watershed Area, Anthony Bell, Stephen J. Jacquemin

Biological Sciences Faculty Publications

A myriad of factors have been shown to influence the morphology offreshwaterfish. However, studies that parse out where variation is comingfrom (e.g. body size, sex, and habitat) as well as what potential thesechanges have to influence function (e.g. swimming performance) areunderstudied. Therefore, the objectives of this study were to describemorphological variation of BluegillLepomis macrochirusacross the GrandLake St Mary’s watershed area (northwest OH, USA) and test forcovariation of morphology with size, sex, and habitat as well as to assessswimming performance to discern whether any differences in habitat (andmorphology) correspond with functional aspects related to criticalswimming velocity. Geometric morphometric methods were used …

First Definitive Fossil Of An Oestroid Fly (Diptera: Calyptratae: Oestroidea) And The Dating Of Oestroid Divergences, Pierfilippo Cerretti, John O. Stireman Iii, Thomas Pape, James E. O'Hara, Marco A. Marinho, Knut Rognes, David A. Grimaldi

Biological Sciences Faculty Publications

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological …

A New Tachinid Genus And Species Record For North America: Iceliopsis Borgmeieri Guimarães, John O. Stireman Iii, Jane E. Dell

Biological Sciences Faculty Publications

The Iceliini are a small, enigmatic New World tribe of Tachininae consisting of three genera, Icelia RobineauDesvoidy, Iceliopsis Guimarães, and Erviopsis Townsend, and five recognized species (Guimarães 1976). All known species are exclusively Neotropical in distribution with the exception of Icelia triquetra (Olivier), which ranges from Brazil, through Central America, and as far north as New York state (O’Hara & Wood 2004). Members of the tribe are generally medium-sized (ca. 7–12 mm), elongate, yellowish or grayish in color, and resemble Dexiini or Leskiini in general appearance. Species of Iceliini are relatively rarely collected and there is but a single host …

Intercellular Adhesion Molecule-1 Augments Myoblast Adhesion And Fusion Through Homophilic Trans-Interactions, Francis X. Pizza, Ryan A. Martin, Evan M. Springer, Maxwell S. Leffler, Bryce R. Woelmer, Issac J. Recker, Douglas W. Leaman

Biological Sciences Faculty Publications

The overall objective of the study was to identify mechanisms through which intercellular adhesion molecule-1 (ICAM-1) augments the adhesive and fusogenic properties of myogenic cells. Hypotheses were tested using cultured myoblasts and fibroblasts, which do not constitutively express ICAM-1, and myoblasts and fibroblasts forced to express full length ICAM-1 or a truncated form lacking the cytoplasmic domain of ICAM-1. ICAM-1 mediated myoblast adhesion and fusion were quantified using novel assays and cell mixing experiments. We report that ICAM-1 augments myoblast adhesion to myoblasts and myotubes through homophilic trans-interactions. Such adhesive interactions enhanced levels of active Rac in adherent and …

Synaptic Up-Scaling Preserves Motor Circuit Output After Chronic, Natural Inactivity, Joseph Michael Santin, Mauricio Vallejo, Lynn K. Hartzler

Biological Sciences Faculty Publications

Neural systems use homeostatic plasticity to maintain normal brain functions and to prevent abnormal activity. Surprisingly, homeostatic mechanisms that regulate circuit output have mainly been demonstrated during artificial and/or pathological perturbations. Natural, physiological scenarios that activate these stabilizing mechanisms in neural networks of mature animals remain elusive. To establish the extent to which a naturally inactive circuit engages mechanisms of homeostatic plasticity, we utilized the respiratory motor circuit in bullfrogs that normally remains inactive for several months during the winter. We found that inactive respiratory motoneurons exhibit a classic form of homeostatic plasticity, up-scaling of AMPA-glutamate receptors. Up-scaling increased the …

Insights Into The Ecology, Genetics And Distribution Of Lucanus Elaphus Fabricius (Coleoptera: Lucanidae), North America's Giant Stag Beetle, Michael D. Ulyshen, Louis G. Zachos, John O. Stireman Iii, Thomas N. Sheehan, Ryan C. Garrick

Biological Sciences Faculty Publications

1. Little is known about the biology or conservation status of Lucanus elaphus Fabricius in North America despite well-documented declines of a related species, Lucanus cervus (L.), in Europe. This study provides information critical to developing conservation plans for L. elaphus including the species’ larval substrate requirements, genetic data and range-wide estimates of habitat suitability. 2. In Mississippi floodplain forests, larval L. elaphus were recovered from a wide range of log sizes and rot types and were either found tunnelling within the wood or feeding beneath logs at the soil–wood interface. The species appears to require 1–2 years to complete …

Network Analytics For The Mirna Regulome And Mirna-Disease Interactions, Joseph Jayakar Nalluri

Theses and Dissertations

miRNAs are non-coding RNAs of approx. 22 nucleotides in length that inhibit gene expression at the post-transcriptional level. By virtue of this gene regulation mechanism, miRNAs play a critical role in several biological processes and patho-physiological conditions, including cancers. miRNA behavior is a result of a multi-level complex interaction network involving miRNA-mRNA, TF-miRNA-gene, and miRNA-chemical interactions; hence the precise patterns through which a miRNA regulates a certain disease(s) are still elusive. Herein, I have developed an integrative genomics methods/pipeline to (i) build a miRNA regulomics and data analytics repository, (ii) create/model these interactions into networks and use optimization techniques, motif …

Biosimp: Using Software Testing Techniques For Sampling And Inference In Biological Organisms, Mikaela Cashman, Jennie L. Catlett, Myra B. Cohen, Nicole R. Buan, Zahmeeth Sakkaff, Massimiliano Pierobon, Christine A. Kelley

School of Computing: Conference and Workshop Papers

Years of research in software engineering have given us novel ways to reason about, test, and predict the behavior of complex software systems that contain hundreds of thousands of lines of code. Many of these techniques have been inspired by nature such as genetic algorithms, swarm intelligence, and ant colony optimization. In this paper we reverse the direction and present BioSIMP, a process that models and predicts the behavior of biological organisms to aid in the emerging field of systems biology. It utilizes techniques from testing and modeling of highly-configurable software systems. Using both experimental and simulation data we show …

Vamorolone, A Dissociative Steroidal Compound, Reduces Pro-Inflammatory Cytokine Expression In Glioma Cells And Increases Activity And Survival In A Murine Model Of Cortical Tumor., Elizabeth Wells, Madhuri Kambhampati, Jesse M Damsker, Heather Gordish-Dressman, Sridevi Yadavilli, Oren J Becher, Jamila Gittens, Mojca Stampar, Roger J. Packer, Javad Nazarian

Genomics and Precision Medicine Faculty Publications

Corticosteroids, such as dexamethasone, are routinely used as palliative care in neuro-oncology for their anti-inflammatory benefits, however many patients experience dose limiting side effects caused by glucocorticoid response element (GRE)-mediated transcription. The purpose of this study was to use a murine model to investigate a new steroid alternative, vamorolone, which promises to reduce side effects through dissociating GRE-mediated transcription and NF-κB -mediated anti-inflammatory actions. To compare vamorolone to dexamethasone in reducing pro-inflammatory signals in vitro, murine glioma cells were treated with dexamethasone, vamorolone or vehicle control. Changes in mRNA expression were assessed using the nanostring inflammatory platform. Furthermore, drug …

Global Gene Expression Profiling Of Healthy Human Brain And Its Application In Studying Neurological Disorders, Simarjeet K. Negi

Theses & Dissertations

The human brain is the most complex structure known to mankind and one of the greatest challenges in modern biology is to understand how it is built and organized. The power of the brain arises from its variety of cells and structures, and ultimately where and when different genes are switched on and off throughout the brain tissue. In other words, brain function depends on the precise regulation of gene expression in its sub-anatomical structures. But, our understanding of the complexity and dynamics of the transcriptome of the human brain is still incomplete. To fill in the need, we designed …

Effect Of Arginine On Oligomerization And Stability Of N-Acetylglutamate Synthase., N Haskins, A Mumo, P H Brown, Mendel Tuchman, Hiroki Morizono, L Caldovic

Genomics and Precision Medicine Faculty Publications

N-acetylglutamate synthase (NAGS; E.C.2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from acetyl coenzyme A and glutamate. In microorganisms and plants, NAG is the first intermediate of the L-arginine biosynthesis; in animals, NAG is an allosteric activator of carbamylphosphate synthetase I and III. In some bacteria bifunctional N-acetylglutamate synthase-kinase (NAGS-K) catalyzes the first two steps of L-arginine biosynthesis. L-arginine inhibits NAGS in bacteria, fungi, and plants and activates NAGS in mammals. L-arginine increased thermal stability of the NAGS-K from Maricaulis maris (MmNAGS-K) while it destabilized the NAGS-K from Xanthomonas campestris (XcNAGS-K). Analytical gel chromatography and ultracentrifugation indicated tetrameric structure of the …

The Effect Of Wee1 On Mitosis In The Spb Mutant, David Leroy

Honors Theses

The speedbump mutant has been identified as an early arrest mutant, becoming apparent as soon as 80% epiboly (8.5 hours of development). This mutant has a mutation in wee1, which is a protein regulating entry into mitosis ensuring the completion of DNA replication before mitosis. The lack of this protein in speedbump allows for early entry into mitosis resulting in damage to the chromosome. Here, we investigate two questions: if mitosis in the speedbump mutant phenotype is more frequent than wild-type phenotype, and, if so, is there a phase in which the mutant phenotype favors. We used phosphorylated histone H3 …

Review Of Booming From The Mists Of Nowhere: The Story Of The Greater Prairie-Chicken By Greg Hoch, Ross H. Hier

The Prairie Naturalist

The Greater Prairie-Chicken (Tympanuchus cupido pinnatus) is an iconic species inhabiting one of the most iconic and rarest habitats in the world—the tallgrass prairies of central North America. To tell the story of the Greater Prairie-Chicken is a monumental task. Its history is intricately woven into pre- and post-European settlement of the North American prairies in such a way that knowledge of the species is spread over several centuries. Thus, researching the “old and the new” regarding the Greater Prairie-Chicken requires a substantial literature review, much of which occurs in publications from the 1800s. Hoch has done a …

Finding The Best Remaining Black Hills Montane Grasslands, The First Step In Conservation, Hollis Marriott, Don Faber-Langendoen, David J. Ode

The Prairie Naturalist

Black Hills Montane Grassland is a rare and endangered plant community endemic to the Black Hills of western South Dakota and northeastern Wyoming. It is restricted to higher elevations on the Limestone Plateau in the western part of the uplift. Early visitors to the Black Hills wrote glowing reports of flower-filled grasslands on the Limestone Plateau. Lieutenant Colonel George A. Custer and his soldiers reveled in lush grass, and decorated the headgear of their horses with flowers (Custer 1875). Expedition botanist A. B. Donaldson “estimated the number of flowers in bloom in Floral Valley at 50, while an equal number …

Changes In The Prairie Naturalist For 2017: Some Bumps In The Road During Transition, Christopher N. Jacques

The Prairie Naturalist

By now it is obvious to most of our members and authors that The Prairie Naturalist (TPN) has experienced some delays in conducting journal-related business over the past few months. Publication of the June 2016 issue was slightly delayed and the December 2016 was mailed much later than planned. So I wanted to update our members on the current status, and other aspects, of TPN. As most of you know, when I transitioned into the Editorship of TPN, one of my first orders of business was to secure a new publication venue for the journal. Fortunately, the Department …

Reproductive Characteristics Of Landlocked Fall Chinook Salmon From Lake Oahe, South Dakota, Kelsen L. Young, Michael E. Barnes, Jeremy L. Kientz

The Prairie Naturalist

Lake Oahe, South Dakota, USA, landlocked fall Chinook salmon (Oncorhynchus tshawytscha) reproductive characteristics were examined over a 27 year period, from 1988 to 2015. Mean total lengths of spawning females ranged from 665 mm (1995) to 812 mm (2015) with considerable year-to-year variation. Post-spawn female weights varied, ranging from 2.02 kg (2000) to 5.55 kg (2015), with an overall mean of 3.04 kg. Fecundity peaked at 4,555 eggs per female in 2003, which was just 3 years after a low of 2,011 eggs per female in 2000. Relative fecundity based on female weight was greatest at 1,211 eggs/kg …

Assessment Of Smallmouth Bass Growth And Mortality In Nebraska Waters, Benjamin J. Schall, Keith D. Koupal, Casey W. Schoenebeck, Keith L. Hurley

The Prairie Naturalist

Smallmouth bass (Micropterus dolomieu) have been introduced across Nebraska into a variety of waterbodies. However, an estimate of smallmouth bass growth and mortality in Nebraska waters has not been produced. The objectives of this study were to use historic sampling data to describe the growth of smallmouth bass in Nebraska lakes in relation to other regional models, growth among waterbody types (reservoirs, Interstate 80 [I-80] lakes, and rivers), estimates of age at quality, preferred, and memorable lengths, and mortality for Nebraska smallmouth bass populations. Mean length ± SE of Nebraska smallmouth bass at age 7 was 383 ± …

Review Of Plants Have So Much To Give Us, All We Have To Do Is Ask: Anishinaabe Botanical Teachings By Mary Siisip Geniusz (Edited By Wendy Makoons Geniusz, Illustrated By Annmarie Geniusz), Natasha Myhal, Kelly Kindscher

The Prairie Naturalist

Plants Have So Much to Give Us, All We Have to Do Is Ask offers a new look at Anishinaabe (Ojibwe) ethnobotany as told through traditional stories. Botanical teachings through stories are a way to pass down traditional knowledge from generation to generation. For example, Anishinaabe knowledge on plants was written and recorded in communities willing to share their knowledge with early scholars, such as Albert B. Reagan (1928), Huron H. Smith (1932), and Melvin R. Gilmore (1933). Each of these scholars spent time with an Anishinaabe community to learn about plants and primarily to provide written descriptions of plants …

Spatial Variation In Germination Of Two Annual Brome Species In The Northern Great Plains, Erin K. Espeland, Jane M. Mangold, Natalie M. West

The Prairie Naturalist

Downy brome or cheat grass (Bromus tectorum L.) and field brome (B. arvensis L.; Synonym = Bromus japonicus Thunb. ex Murr.; Japanese brome) are two annual exotic species that have increased the intensity and frequency of fire cycles in the Intermountain West of the United States, with millions of dollars in associated costs (DiTomaso 2000). These invasive brome species have a different impact in the Northern Great Plains of North America where they commonly co-occur in disturbed sites (White and Currie 1983, Haferkamp et al. 1993). In these mixed-grass prairie rangelands, annual bromes compete against other forage species …

Review Of Waterfowl Of North America, Europe, And Asia: An Identification Guide By Sébastien Reeber, William L. Hohman

The Prairie Naturalist

Ducks, geese and swans (Family Anatidae) are the most popular and best studied group of birds in the world. The group has been the subject of classical books by Kortright (1942), Delacour (1954-1964), Bellrose (1976), Palmer (1976), Johnsgard (1978), and, most recently, Kear (2005) and Baldassarre (2014). The latest contribution to this rich legacy is an impressively illustrated identification guide for waterfowl found in North America, Europe and Asia by author and artist, Sébastien Reeber. This is an English-language version of Canards, Cygnes et Oies d’Europe, d’Asie et d’Amérique du Nord, published by Delachaux and Niestlé in late 2015. …

Review Of Birds Of Montana By Jeffrey S. Marks, Paul Hendricks, And Daniel Casey, Scott G. Somershoe

The Prairie Naturalist

The Birds of Montana is an impressive-looking tome, that includes 659 pages, 155 color range maps, 73 illustrations of species, and 16 color photos of Montana’s habitats. Upon the first bend of the binding, the reader will quickly realize the impressive depth of detail and research that went into writing and completing this book. Although Montana is the fourth largest state, one of the least populated states, and has few “binoculars on the ground,” the state has a fascinating and extensive ornithological history. The Birds of Montana is not a field guide, but rather it is an astonishingly comprehensive reference …

Review Of Estimation Of Parameters For Animal Populations: A Primer For The Rest Of Us By Larkin A. Powell And George A. Gale, Max Post Van Der Burg

The Prairie Naturalist

“Me? A modeler? Never!” This is the opening challenge of the book, Estimation of Parameters for Animal Populations: A Primer for the Rest of Us, by Larkin Powell and George Gale. I say “challenge” because I think this book attempts to challenge the misconception that quantitative methods are out of reach for most biologists and wildlife scientists. When many of us attend college or graduate school to study wildlife science there’s a sense that, at some point, there will be math. But it appears that the attitude of many students toward this reality is to simply suffer through the …

Network Inference Driven Drug Discovery, Gergely Zahoránszky-Kőhalmi, Tudor I. Oprea, Cristian G. Bologa, Subramani Mani, Oleg Ursu

Biomedical Sciences ETDs

The application of rational drug design principles in the era of network-pharmacology requires the investigation of drug-target and target-target interactions in order to design new drugs. The presented research was aimed at developing novel computational methods that enable the efficient analysis of complex biomedical data and to promote the hypothesis generation in the context of translational research. The three chapters of the Dissertation relate to various segments of drug discovery and development process.

The first chapter introduces the integrated predictive drug discovery platform „SmartGraph”. The novel collaborative-filtering based algorithm „Target Based Recommender (TBR)” was developed in the framework of this …

Zombies, Predatory Wasps And Consciousness, James K. Peterson

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Harpy Eagle (Harpia Harpyja) Conservation: Juvenile Behavior And Diet At A Nest Near Pijibasal, Darien, Hannah Rodgers

Independent Study Project (ISP) Collection

The Harpy Eagle (Harpia harpyja), the largest and most powerful bird of prey in the Americas, is declining throughout its range in Neotropical forests. Hunting and deforestation threaten populations in the most important remaining eagle habitat in Central America, the Darien province of Panama. These eagles may have the longest postfledging juvenile dependency of any raptor, though juvenile behavior during this period is poorly studied. This study monitored an 11-month-old juvenile for 7 days at a nest near the indigenous community of Pijibasal in order to study behavior and diet. Researchers recorded the juvenile’s location and behavior, studied prey remains …

Identification Of Control Targets In Boolean Molecular Network Models Via Computational Algebra, David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Reinhard Laubenbacher

Mathematics Faculty Publications

Background: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type …