Systems Biology Commons^™

Identification Of Host Factors Required For Yersinia Pestis Macrophage Intracellular Survival And Their Impact On Vacuole Maturation, Acidification And Trafficking., Michael Graylin Connor

Electronic Theses and Dissertations

Y. pestis is a facultative intracellular pathogen and the causative agent of plague. This bacterium, while most noted or the Black Death during the European 14^th century, is not a historic pathogen but a re-emerging pandemic with both domestic and global impact. Y. pestis is capable of colonizing the macrophage, and actively subverts phagolysosome maturation to establish a replicative niche known as the Yersinia containing vacuole (YCV). The exploited host factors required to support the YCV are unknown. Here we identified a comprehensive list of host factors required for Y. pestis survival through a genome-wide RNAi high-throughput screen. We …

A Tale Of Two Theories: Using An Engineered Strain Of E. Coli To Bridge The Gap Between Quorum Sensing And Diffusion Sensing, Cortney E. Wilson

HCNSO Student Theses and Dissertations

Cooperation is a trait that is found at all levels of biological organization. Interestingly, cooperation appears to occur in bacteria that produce small, easily diffusible molecules called autoinducers. To understand why bacteria produce these autoinducers, the scientific community has focused on one predominant theory called quorum sensing. Under this theory, bacteria produce autoinducers so they can sense the density of the population. Once a sufficiently high population density is reached, autoinducers initiate the production of a costly gene product that serves to benefit the population. In contrast, a competing theory called diffusion sensing suggests that autoinducers are used by the …

Design Science 5 | Steam Intelligence, Schedule, Edna W. Lawrence Nature Lab

Design Science Symposia

Schedule of events.

Photocatalytic Reduction Of Fumarate To Succinate On Zns Mineral Surfaces, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

The reductive tricarboxylic acid (rTCA) cycle is an important central biosynthetic pathway that fixes CO₂ into carboxylic acids. Among the five reductive steps in the rTCA cycle, the two-electron reduction of fumarate to succinate proceeds nonenzymatically on the surface of photoexcited sphalerite (ZnS) colloids suspended in water. This model reaction is chosen to systematically study the surface photoprocess occurring on ZnS in the presence of [Na₂S] (1–10 mM) hole scavenger at 15 °C. Experiments at variable pH (5–10) indicate that monodissociated fumaric acid is the primary electron acceptor forming the monoprotic form of succinic acid. The following …

Nutrient Cycling In The Amazon: A Comparison Of Soil Characteristics, Insects, Root Types And Decomposition Rates Between Varzea And Terra Firme Habitats In The Ecuadorian Amazon, Mira Ensley-Field

Independent Study Project (ISP) Collection

Decomposition and nutrient cycling form the basis of every ecosystem. Nutrient availability in the soil affects plant species composition, richness, and productivity. The Amazon rainforest is known for its unusually fast nutrient cycle, but many aspects lack detailed study and analysis. This comparative study carried out in the Ecuadorian Amazon had four primary objectives related to understanding the nutrient cycle in the Amazon; 1.) analyze soil characteristics, 2.) assess insect diversity in the leaf litter layer, 3.) examine root characteristics, and 4.) measure the decomposition rate between Varzea and Terra Firme habitats alongside the Rio Napo. Forty 0.25 x 0.25m …

New Clues To A Mass Extinction: Colby Geologist Robert Gastaldo And Student Researchers Unearth Evidence That Contradicts Prevailing Models About Ancient Die-Offs, Stephen Collins

Colby Magazine

Colby geologists are rewriting deep time history, altering the script of how scientists understand the mother of all mass extinctions—the End-Permian event that occurred approximately 252 million years ago. Or to suggest that they don’t, in fact, understand it.

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function …

Associations Between Ectomycorrhizal Fungi And Bacterial Needle Endophytes In Pinus Radiata: Implications For Biotic Selection Of Microbial Communities, Megan A. Rúa, Emily C. Wilson, Sarah Steele, Arielle R. Munters, Jason D. Hoeksema, Anna C. Frank

Biological Sciences Faculty Publications

Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. …

A Continental Analysis Of Ecosystem Vulnerability To Atmospheric Nitrogen Deposition, Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop, Donald M. Waller

Biological Sciences Faculty Research

Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg N·ha …

Editorial: Systems Biology And Ecology Of Microbial Mat Communities, Martin G. Klotz, Donald A. Bryant, Jim K. Fredrickson, William P. Inskeep, Michael Kühl

Publications and Research

No abstract provided.

Late Pleistocene Fishes Of The Tennessee River Basin: An Analysis Of A Late Pleistocene Freshwater Fish Fauna From Bell Cave (Site Acb-2) In Colbert County, Alabama, Usa, Stephen J. Jacquemin, Jun A. Ebersole, William C. Dickenson, Charles Ciampaglio

Biological Sciences Faculty Publications

The Tennessee River Basin is considered one of the most important regions for freshwater biodiversity anywhere on the globe. The Tennessee River Basin currently includes populations of at least half of the described contemporary diversity of extant North American freshwater fishes, crayfish, mussel, and gastropod species. However, comparatively little is known about the biodiversity of this basin from the Pleistocene Epoch, particularly the late Pleistocene (∼10,000 to 30,000 years B.P.) leading to modern Holocene fish diversity patterns. The objective of this study was to describe the fish assemblages of the Tennessee River Basin from the late Pleistocene using a series …

Parts Of The Whole: Teaching Quantitative Reasoning In The Predator-Prey Model, Dorothy Wallace

Numeracy

The classical predator-prey equations are in nearly every differential equations text and mathematical biology text. Usually they are presented fait accompli, leaving the student to analyze them or play with a computer program. Here we show that the process of fully understanding where these equations come from and how they are derived provides numerous opportunities to teach or reinforce quantitative reasoning skills necessary to future scientists. This example is used to invoke logic, systems thinking, causal reasoning, understanding functions of one or more variables, quantities versus rates of change, proportional reasoning, unit analysis, and comparison to data.

Metataxonomic And Metagenomic Approaches Vs. Culture-Based Techniques For Clinical Pathology., Sarah K. Hilton, Eduardo Castro-Nallar, Marcos Pérez-Losada, Ian Toma, Timothy A. Mccaffrey, Eric P. Hoffman, Marc O. Siegel, Gary L. Simon, W. Evan Johnson, Keith Crandall

Genomics and Precision Medicine Faculty Publications

Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five …

Effect Of The Il-1 Receptor Antagonist Kineret® On Disease Phenotype In Mdx Mice., Margaret E. Benny Klimek, Arpana Sali, Sree Rayavarapu, Jack Van Der Meulen, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

Duchenne muscular dystrophy (DMD) is an X-linked muscle disease caused by mutations in the dystrophin gene. The pathology of DMD manifests in patients with progressive muscle weakness, loss of ambulation and ultimately death. One of the characteristics of DMD is muscle inflammation, and dystrophin-deficient skeletal muscles produce higher levels of the pro-inflammatory cytokine interleukin 1β (IL-1β) in response to toll like receptor (TLR) stimulation compared to controls; therefore, blocking the IL-1β pathway could improve the disease phenotype in mdx mice, a mouse model of DMD. Kineret® or IL-1Ra is a recombinant IL-1 receptor antagonist approved by the FDA for treating …

Glucocorticoid Receptor (Nr3c1) Variants Associate With The Muscle Strength And Size Response To Resistance Training., Garrett I Ash, Matthew A Kostek, Harold Lee, Theodore J Angelopoulos, Priscilla M Clarkson, Paul M Gordon, Niall M Moyna, Paul S Visich, Robert F Zoeller, Thomas B Price, Joseph M. Devaney, Heather Gordish-Dressman, Paul D Thompson, Eric P. Hoffman, Linda S Pescatello

Genomics and Precision Medicine Faculty Publications

Glucocorticoid receptor (NR3C1) polymorphisms associate with obesity, muscle strength, and cortisol sensitivity. We examined associations among four NR3C1 polymorphisms and the muscle response to resistance training (RT). European-American adults (n = 602, 23.8±0.4yr) completed a 12 week unilateral arm RT program. Maximum voluntary contraction (MVC) assessed isometric strength (kg) and MRI assessed biceps size (cm2) pre- and post-resistance training. Subjects were genotyped for NR3C1 -2722G>A, -1887G>A, -1017T>C, and +363A>G. Men carrying the -2722G allele gained less relative MVC (17.3±1.2vs33.5±6.1%) (p = 0.010) than AA homozygotes; men with -1887GG gained greater relative MVC than A allele carriers …

Effects On Muscle Tissue Remodeling And Lipid Metabolism In Muscle Tissue From Adult Patients With Polymyositis Or Dermatomyositis Treated With Immunosuppressive Agents., Ingela Loell, Joan Raouf, Yi-Wen Chen, Rongye Shi, Inger Nennesmo, Helene Alexanderson, Maryam Dastmalchi, Kanneboyina Nagaraju, Marina Korotkova, Ingrid E Lundberg

Genomics and Precision Medicine Faculty Publications

BACKGROUND: Polymyositis (PM) and dermatomyositis (DM) are autoimmune muscle diseases, conventionally treated with high doses of glucocorticoids in combination with immunosuppressive drugs. Treatment is often dissatisfying, with persisting muscle impairment. We aimed to investigate molecular mechanisms that might contribute to the persisting muscle impairment despite immunosuppressive treatment in adult patients with PM or DM using gene expression profiling of repeated muscle biopsies.

METHODS: Paired skeletal muscle biopsies from six newly diagnosed adult patients with DM or PM taken before and after conventional immunosuppressive treatment were examined by gene expression microarray analysis. Selected genes that displayed changes in expression were analyzed …

Identification Of Lead-Sensitive Expression And Splicing Quantitative Trait Loci In Drosophila Melanogaster By Analysis Of Rna-Seq Data, Wen Qu

Wayne State University Dissertations

Lead exposure has long been one of the most important topics in global public health since it is a potent developmental neurotoxin. Here, we conducted an expression QTL (eQTLs) analysis, which is genome-wide association analysis of genetic variants with differential gene expression, in the male heads of 79 Drosophila melanogaster recombinant inbred lines originally from eight parental strains in the presence or absence of developmental exposure to 250 µM lead acetate. The aim was to study the effects of lead exposure on gene expression and identify the lead-responsive genes. After detecting 1,536 cis-eQTLs and 952 trans-eQTLs (1000 permutation threshold at …

A Century Of Morphological Variation In Cyprinidae Fishes, Stephen J. Jacquemin, Mark Pyron

Biological Sciences Faculty Publications

Background

Aquatic habitats have been altered over the past century due to a variety of anthropogenic influences. Ecomorphology is an area of aquatic ecology that can both directly and indirectly assess the effects of habitat alterations on organisms. However, few studies have explored long term trends in morphological variation. Long term changes in morphology can potentially impact niche and ultimately contribute to organismal success and the ecosystem. Therefore, in this study we assessed long term morphological variation with body size, sex, time, and hydrology using museum collections of five species of Cyprinidae (Minnows) from lentic and lotic systems over the …

Fidelity And Survival Of Breeding Mallards In The Nebraska Sandhills, Zachary J. Cunningham, Larkin Powell, Mark P. Vrtiska

The Prairie Naturalist

Assessment of demographic parameters of a population allows managers to better understand factors affecting populations and increase efficiency of conservation efforts. Few data on demographics exist for mallards (Anas platyrhynchos) breeding in the Nebraska Sandhills. Thus, we used banding data to estimate probabilities of fidelity, survival, band recovery, and recapture of mallards banded in the eastern Sandhills, 2005–2008. Our recapture probability estimate for mallards was 0.074 (95% CI: 0.033–0.158), and the recovery probability estimate was 0.300 (95% CI: 0.156–0.497). Mallard annual survival was 0.795 (95% CI: 0.609–0.906) with a fidelity probability of 0.618 (95% CI: 0.283–0.868). High annual …

Review Of Following The Wild Bees: The Craft And Science Of Bee Hunting By Thomas D. Seeley, Katrina Klett

The Prairie Naturalist

Since the media’s coverage of the sudden losses of worker bee populations in many honeybee colonies during the winter of 2006-07 (a phenomenon that was later termed the Colony Collapse Disorder or CCD), there have been increasingly high levels of popular interest in bees and beekeeping in the United States. While a number of books have followed this wave of interest, Following the Wild Bees: The Craft and Science of Bee Hunting by Thomas Seeley is a fundamentally unique contribution to popular honeybee literature. The focus of the book is not on the current synergy of effects that are leading …

Evidence For Use Of Alliaria Petiolata In North America By The European Cabbage White Butterfly, Pieris Rapae, Sam L. Davis, Don Cipollini

Biological Sciences Faculty Publications

Pieris rapae L., an invasive crop pest, may have recently begun using Alliaria petiolata Bieb. (Cavara & Grande), a European invasive biennial. We investigated how P. rapae uses forest habitats for nectar and oviposition and examined larval performance on A. petiolata in the field and laboratory. Being known primarily to occupy open habitats, we found that P. rapae regularly uses forest edge habitats, most surveyed A. petiolata plants had P. rapae damage, and P. rapae successfully used both stages of A. petiolata for larval development.

Home-Field Advantage? Evidence Of Local Adaptation Among Plants, Soil, And Arbuscular Mycorrhizal Fungi Through Meta-Analysis, Megan A. Rúa, Anita Antoninka, Pedro M. Antunes, V. Bala Chaudhary, Catherine Gehring, Louis J. Lamit, Bridget J. Piculell, James D. Bever, Cathy Zabinski, James F. Meadow, Marc J. Lajeunesse, Brook G. Milligan, Justine Karst, Jason D. Hoeksema

Biological Sciences Faculty Publications

Background: Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactions may be particularly important for plants, as they associate with microbial symbionts that can significantly affect their fitness and may enable rapid evolution. The arbuscular mycorrhizal (AM) symbiosis is ideal for investigations of local adaptation because it is globally widespread among most plant taxa and can significantly affect plant growth and fitness. Using meta-analysis on 1170 studies …

Twenty-Five Year Response Of The Herbaceous Layer Of A Temperate Hardwood Forest To Elevated Nitrogen Deposition, Frank S. Gilliam, Nicole Turrill Welch, Anne Hockenberry Phillips, Jake H. Billmyer, William T. Peterjohn, Zachariah K. Fowler, Christopher A. Walter, Mark B. Burnham, Jeffrey D. May, Mary Beth Adams

Biological Sciences Faculty Research

Increasing rates of atmospheric deposition of nitrogen (N) present a novel threat to the biodiversity of terrestrial ecosystems. Many forests are particularly susceptible to excess N given their proximity to sources of anthropogenic N emissions. This study summarizes results of a 25-yr treatment of an entire central Appalachian hardwood forest watershed via aerial applications of N with a focus on effects of added N on the cover, species richness, and composition of the herbaceous layer. Research was carried out on two watersheds of the Fernow Experimental Forest (FEF), West Virginia. The long-term reference watershed at FEF (WS4) was used as …

Epigenetics And Shared Molecular Processes In The Regeneration Of Complex Structures, Labib Rouhana, Junichi Tasaki

Biological Sciences Faculty Publications

The ability to regenerate complex structures is broadly represented in both plant and animal kingdoms. Although regenerative abilities vary significantly amongst metazoans, cumulative studies have identified cellular events that are broadly observed during regenerative events. For example, structural damage is recognized and wound healing initiated upon injury, which is followed by programmed cell death in the vicinity of damaged tissue and a burst in proliferation of progenitor cells. Sustained proliferation and localization of progenitor cells to site of injury give rise to an assembly of differentiating cells known as the regeneration blastema, which fosters the development of new tissue. Finally, …

Tachinid Collecting In Temperate South America. Expeditions Of The Phylogeny Of World Tachinide Project. Part Iii. Chile, John O. Stireman Iii, James E. O'Hara, Pierfilippo Cerretti, Diego J. Inclán

Biological Sciences Faculty Publications

As readers of this newsletter are likely familiar, we and our collaborators have been working for the past several years on a family-wide phylogeny of the Tachinidae of the world (see Stireman et al. 2013, Winkler et al. 2014). We have already published a morphological analysis of tachinid phylogenetics (Cerretti et al. 2014), as well as an initial molecular phylogenetic framework for the family (Winkler et al. 2015). An in-depth molecular phylogenetic analysis of the Phasiinae led by Jeremy Blaschke (originally at University of Tennessee and now at Union University, TN) and Kevin Moulton (U. of Tenn.) is currently being …

Transcriptome Analysis Of Vaccine Responses To Francisella Tularensis Or Venezuelan Equine Encephalitis Virus, Rebecca Ann Erwin-Cohen

Walden Dissertations and Doctoral Studies

The lack of vaccines for emerging and re-emerging diseases highlights technical gaps and indicates a need for innovative approaches to produce new vaccines. Vaccines may be improved by knowledge of host responses to vaccination, disease pathogenesis, and the effect of age and genetics on vaccine outcome. This study's purpose was to quantitatively assess the molecular epidemiology of Francisella tularensis (Ft) and Venezuelan Equine Encephalitis Virus (VEEV). Study results support the Epidemiology Nexus model which holds that association of changes in gene expression to vaccination facilitate understanding the mechanisms of immune development and link public health and disease epidemiology. My research …

A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris

Theses and Dissertations

The decreasing costs of next generation sequencing technologies and the increasing speeds at which they work have lead to an abundance of 'omic datasets. The need for tools and methods to analyze, annotate, and model these datasets to better understand biological systems is growing. Here we present a novel software pipeline to reconstruct the metabolic model of an organism in silico starting from its genome sequence and a novel compilation of biological databases to better serve the generation of metabolic models. We validate these methods using five Gardnerella vaginalis strains and compare the gene annotation results to NCBI and the …

Synthesis Of Satellite Microwave Observations For Monitoring Global Land-Atmosphere Co2 Exchange, Lucas Alan Jones

Graduate Student Theses, Dissertations, & Professional Papers

This dissertation describes the estimation, error quantification, and incorporation of land surface information from microwave satellite remote sensing for modeling global ecosystem land-atmosphere net CO₂ exchange. Retrieval algorithms were developed for estimating soil moisture, surface water, surface temperature, and vegetation phenology from microwave imagery timeseries. Soil moisture retrievals were merged with model-based soil moisture estimates and incorporated into a light-use efficiency model for vegetation productivity coupled to a soil decomposition model. Results, including state and uncertainty estimates, were evaluated with a global eddy covariance flux tower network and other independent global model- and remote-sensing based products.

Mitochondrial Function Assessed By 31p Mrs And Bold Mri In Non-Obese Type 2 Diabetic Rats, Yuchi Liu, Xunbai Mei, Jielei Li, Nicola Lai, Xin Yu

Electrical & Computer Engineering Faculty Publications

The study aims to characterize age-associated changes in skeletal muscle bioenergetics by evaluating the response to ischemia-reperfusion in the skeletal muscle of the Goto-Kakizaki (GK) rats, a rat model of non-obese type 2 diabetes (T2D). ³¹P magnetic resonance spectroscopy (MRS) and blood oxygen level-dependent (BOLD) MRI was performed on the hindlimb of young (12 weeks) and adult (20 weeks) GK and Wistar (control) rats. ³¹P-MRS and BOLD-MRI data were acquired continuously during an ischemia and reperfusion protocol to quantify changes in phosphate metabolites and muscle oxygenation. The time constant of phosphocreatine recovery, an index of mitochondrial oxidative capacity, …

Suppression Of F1 Male-Specific Lethality In Caenorhabditis Hybrids By Cbr-Him-8, Vaishnavi Ragavapuram, Emily Elaine King, Scott Everet Baird

Biological Sciences Faculty Publications

Haldane's Rule and Darwin's Corollary to Haldane's Rule are the observations that heterogametic F1 hybrids frequently are less fit than their homogametic siblings and that asymmetric results often are obtained from reciprocal hybrid crosses. In Caenorhabditis, Haldane's Rule and Darwin's Corollary have been observed in several hybrid crosses, including crosses of Caenorhabditis briggsae and Caenorhabditis nigoni. Fertile F1 females are obtained from reciprocal crosses. However, F1 males obtained from C. nigoni mothers are sterile and F1 males obtained from C. briggsae die during embryogenesis. We have identified cbr-him-8 as a recessive maternal-effect suppressor of F1 hybrid male-specific lethality …