Systems Biology Commons^™

The Equitable Contributions Of Environment, Management And Restoration Status On Grassland Diversity And Composition, Raeann C. Powers

School of Biological Sciences: Dissertations, Theses, and Student Research

Plant composition is controlled by a combination of environmental, biotic, historical and management factors. Although there has been much focus on restoring grassland diversity, it is unclear which factors and/or interactions of factors are constraining diversity in grasslands and the relative influences of different factors. We measured soil fertility, soil texture, grazing intensity, fire frequency and plant cover in 694 plots, located within 33 remnant and restored fields in managed grasslands in the central Great Plains. Using univariate (general linear model) and multivariate (PERMANOVA) analyses, we identified significant factors and their relative contributions to plant richness, evenness, floristic quality index …

Body Size And Geographic Range Do Not Explain Long Term Variation In Fish Populations: A Bayesian Phylogenetic Approach To Testing Assembly Processes In Stream Fish Assemblages, Stephen J. Jacquemin, Jason C. Doll

Biological Sciences Faculty Publications

We combine evolutionary biology and community ecology to test whether two species traits, body size and geographic range, explain long term variation in local scale freshwater stream fish assemblages. Body size and geographic range are expected to influence several aspects of fish ecology, via relationships with niche breadth, dispersal, and abundance. These traits are expected to scale inversely with niche breadth or current abundance, and to scale directly with dispersal potential. However, their utility to explain long term temporal patterns in local scale abundance is not known. Comparative methods employing an existing molecular phylogeny were used to incorporate evolutionary relatedness …

High Hiv Incidence In The Postpartum Period Sustains Vertical Transmission In Settings With Generalized Epidemics: A Cohort Study In Southern Mozambique, Caroline De Schacht, Nedia Mabunda, Orlando C. Ferreira Jr., Nalia Ismael, Nurbai Calu, Iolanda Santos, Heather J. Hoffman, Catharina Alons, Laura Guay, Ilesh V. Jani

Genomics and Precision Medicine Faculty Publications

Introduction: Acute infection with HIV in the postpartum period results in a high risk of vertical transmission through breastfeeding. A study was done to determine the HIV incidence rate and associated risk factors among postpartum women in Southern Mozambique, where HIV prevalence among pregnant women is 21%.

Methods: A prospective cohort study was conducted in six rural health facilities in Gaza and Maputo provinces from March 2008 to July 2011. A total of 1221 women who were HIV-negative on testing at delivery or within two months postpartum were recruited and followed until 18 months postpartum. HIV testing, collection …

Host Specificity And Co-Speciation In Avian Haemosporidia In The Western Cape, South Africa, Sharon Okanga, Graeme S. Cumming, Philip A.R. Hockey, Lisa Nupen, Jeffrey L. Peters

Biological Sciences Faculty Publications

Host and pathogen ecology are often closely linked, with evolutionary processes often leading to the development of host specificity traits in some pathogens. Host specificity may range from ‘generalist’, where pathogens infect any available competent host; to ‘specialist’, where pathogens repeatedly infect specific host species or families. Avian malaria ecology in the region remains largely unexplored, despite the presence of vulnerable endemic avian species. We analysed the expression of host specificity in avian haemosporidia, by applying a previously developed host specificity index to lineages isolated from wetland passerines in the Western Cape, South Africa. Parasite lineages were isolated using PCR …

Expression Pattern And Biochemical Properties Of Zebrafish N-Acetylglutamate Synthase, Ljubica Caldovic, Nantaporn Haskins, Amy Mumo, Himani Majumdar, Mary Pinter, Mendel Tuchman, Alison Krufka

Genomics and Precision Medicine Faculty Publications

The urea cycle converts ammonia, a waste product of protein catabolism, into urea. Because fish dispose ammonia directly into water, the role of the urea cycle in fish remains unknown. Six enzymes, N-acetylglutamate synthase (NAGS), carbamylphosphate synthetase III, ornithine transcarbamylase, argininosuccinate synthase, argininosuccinate lyase and arginase 1, and two membrane transporters, ornithine transporter and aralar, comprise the urea cycle. The genes for all six enzymes and both transporters are present in the zebrafish genome. NAGS (EC 2.3.1.1) catalyzes the formation of N-acetylglutamate from glutamate and acetyl coenzyme A and in zebrafish is partially inhibited by L-arginine. NAGS and other urea …

Patch Burn‐Grazing: An Annotated Bibliography, Rajeeva Voleti, Stephen L. Winter, Sherry Leis

School of Natural Resources: Faculty Publications

Patch burn‐grazing is a rangeland management strategy that exploits the attraction of grazing animals to recently burned areas in order to achieve management objectives. When fire is applied to a landscape in a patchy manner, leaving some patches unburned, the resulting grazing animal activity, forage utilization, and animal impact are patchily distributed within that landscape as well. Areas that have been recently burned tend to be characterized by the highest levels of grazing animal activity while areas that have gone the longest without burning tend to be characterized by the lowest levels of grazing animal activity. This can be advantageous …

Dysferlin Regulates Cell Membrane Repair By Facilitating Injury-Triggered Acid Sphingomyelinase Secretion, Aurelia Defour, Jack H. Van Der Meulen, Rujuta R. Bhatt, Anne Bigot, R. Bashir, Kanneboyina Nagaraju, Jyoti K. Jaiswal

Genomics and Precision Medicine Faculty Publications

Dysferlin deficiency compromises the repair of injured muscle, but the underlying cellular mechanism remains elusive. To study this phenomenon, we have developed mouse and human myoblast models for dysferlinopathy. These dysferlinopathic myoblasts undergo normal differentiation but have a deficit in their ability to repair focal injury to their cell membrane. Imaging cells undergoing repair showed that dysferlin-deficit decreased the number of lysosomes present at the cell membrane, resulting in a delay and reduction in injury-triggered lysosomal exocytosis. We find repair of injured cells does not involve formation of intracellular membrane patch through lysosome–lysosome fusion; instead, individual lysosomes fuse with the …

Knowledge-Fused Differential Dependency Network Models For Detecting Significant Rewiring In Biological Networks, Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Wang

Genomics and Precision Medicine Faculty Publications

Background

Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a …

Non-Invasive Mri And Spectroscopy Of Mdx Mice Reveal Temporal Changes In Dystrophic Muscle Imaging And In Energy Deficits., Christopher R. Heier, Alfredo D. Guerron, Alexandru Korotcov, Stephen Lin, Heather Gordish-Dressman, Stanley Fricke, Raymond W. Sze, Eric P. Hoffman, Paul Wang, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

In Duchenne muscular dystrophy (DMD), a genetic disruption of dystrophin protein expression results in repeated muscle injury and chronic inflammation. Magnetic resonance imaging shows promise as a surrogate outcome measure in both DMD and rehabilitation medicine that is capable of predicting clinical benefit years in advance of functional outcome measures. The mdx mouse reproduces the dystrophin deficiency that causes DMD and is routinely used for preclinical drug testing. There is a need to develop sensitive, non-invasive outcome measures in the mdx model that can be readily translatable to human clinical trials. Here we report the use of magnetic resonance imaging …

Progress Towards A Molecular Phylogeny Of Tachinidae, Year Two, Isaac S. Winkler, John O. Stireman Iii, John K. Moulton, Pierfilippo Cerretti, Jeremy D. Blaschke

Biological Sciences Faculty Publications

We reported last year (Stireman et al. 2013) in The Tachinid Times on our collaborative project, funded by the U.S. National Science Foundation, to study the phylogeny of Tachinidae on a worldwide scale. Since that report, we have made some significant progress towards our goal of assembling a robust phylogenetic tree for Tachinidae. Notably, Cerretti et al. (in press) completed a phylogenetic study using 135 morphological characters from 180 tachinid genera. Results from this study largely reflect, with some interesting exceptions, what we are finding from preliminary analyses of our molecular data. Although sampling of taxa and genes for the …

Native Insect Herbivory Limits Population Growth Rate Of A Non-Native Thistle, James O. Eckberg, Brigitte Tenhumberg, Svata M. Louda

Brigitte Tenhumberg Papers

The influence of native fauna on non-native plant population growth, size, and distribution is not well documented. Previous studies have shown that native insects associated with tall thistle (Cirsium altissimum) also feed on the leaves, stems, and flower heads of the Eurasian congener Cirsium vulgare, thus limiting individual plant performance. In this study, we tested the effects of insect herbivores on the population growth rate of C. vulgare. We experimentally initiated invasions by adding seeds at four unoccupied grassland sites in eastern Nebraska, USA, and recorded plant establishment, survival, and reproduction. Cumulative foliage and floral herbivory …

Piwi Homologs Mediate Histone H4 Mrna Localization To Planarian Chromatoid Bodies, Labib Rouhana, Jennifer A. Weiss, Ryan S. King, Phillip A. Newmark

Biological Sciences Faculty Publications

The well-known regenerative abilities of planarian flatworms are attributed to a population of adult stem cells called neoblasts that proliferate and differentiate to produce all cell types. A characteristic feature of neoblasts is the presence of large cytoplasmic ribonucleoprotein granules named chromatoid bodies, the function of which has remained largely elusive. This study shows that histone mRNAs are a common component of chromatoid bodies. Our experiments also demonstrate that accumulation of histone mRNAs, which is typically restricted to the S phase of eukaryotic cells, is extended during the cell cycle of neoblasts. The planarian PIWI homologs SMEDWI-1 and SMEDWI-3 are …

Chasing Tachinids ‘Down Under’: Expeditions Of The Phylogeny Of World Tachinidae Project, Part Ii Eastern Australia, James E. O'Hara, Pierfilippo Cerretti, John O. Stireman Iii, Isaac S. Winkler

Biological Sciences Faculty Publications

Last year we documented in the pages of this newsletter an expedition to the Western Cape of South Africa in search of tachinids for the “Phylogeny of World Tachinidae” project (Cerretti et al. 2013). The project itself was discussed in a separate article (Stireman et al. 2013). In this issue of The Tachinid Times we discuss our expedition to eastern Australia in late 2013. This trip took place so recently that we have yet to fully identify our material and as a result cannot record here all of the taxa we collected. Instead, we will add the taxa to a …

Is There Light After Depth? Distribution Of Periphyton Chlorophyll And Productivity In Lake Littoral Zones, Yvonne Vadeboncoeur, Shawn P. Devlin, Peter B. Mcintyre, M. J. Vander Zanden

Biological Sciences Faculty Publications

Periphyton and phytoplankton contribute to the base of lake food webs, and both groups of microalgae are influenced by resources and physical forcing. Spatial variation in light availability interacts with the physical dynamics of the water column to create predictable depth gradients in resources and disturbance that may differentially affect periphyton vs phytoplankton. We characterized the depth distribution of chlorophyll and productivity of periphyton on sediments (epipelon) and phytoplankton in the euphotic zones of 13 oligomesotrophic lakes that span a large size gradient (0.017–32,600 km²). Epipelic chlorophyll usually increased with depth in the epilimnion. Light was the primary …

Why Is Living Fast Dangerous? Disentangling The Roles Of Resistance And Tolerance Of Disease, James P. Cronin, Megan A. Rúa, Charles E. Mitchell

Biological Sciences Faculty Publications

Primary axes of host developmental tempo (HDT; e.g., slow-quick return continuum) represent latent biological processes and are increasingly used to a priori identify hosts that contribute disproportionately more to pathogen transmission. The influence of HDT on host contributions to transmission depends on how HDT influences both resistance and tolerance of disease. Here, we use structural equation modeling to address known limitations of conventional measures of resistance and tolerance. We first provide a general resistance-tolerance metamodel from which system-specific models can be derived. We then develop a model specific to a group of vector-transmitted viruses that infect hundreds of grass species …

Sampling Local Fungal Diversity In An Undergraduate Laboratory Using Dna Barcoding, A. H. Harrington, A. F. Bigott, B. W. Anderson, M. J. Boone, S. M. Brick, J. F. Delsol, R. A. Hotchkiss, R. A. Huddleston, E. H. Kasper, J. J. Mcgrady, M. L. Mckinnie, M. V. Ottenlips, N. E. Skinner, K. C. Spatz, A. J. Steinberg, F. Van Den Broek, C. N. Wilson, A. M. Wofford, A. M. Willyard

Journal of the Arkansas Academy of Science

Traditional methods for fungal species identification require diagnostic morphological characters and are often limited by the availability of fresh fruiting bodies and local identification resources. DNA barcoding offers an additional method of species identification and is rapidly developing as a critical tool in fungal taxonomy. As an exercise in an undergraduate biology course, we identified 9 specimens collected from the Hendrix College campus in Conway, Arkansas, USA to the genus or species level using morphology. We report that DNA barcoding targeting the internal transcribed spacer (ITS) region supported several of our taxonomic determinations and we were able to contribute 5 …

Rates And Modes Of Sequence Evolution In Various Lineages Within Chenopodiaceae, James Andrew Naeger

Wayne State University Theses

Sexual dimorphism in domesticated spinach, Spinacia oleracea, is thought to be determined by differential expression of floral organ identity genes. We examined the floral organ morphologies of seven species in the Chenopodiaceae, including two wild species of spinach, in order to gain insight into the evolution of floral reproductive strategy in this clade. The species within the Anserineae demonstrate extensive evolution in floral morphology and reproductive strategy, and Spinacia is unique for having been domesticated rather recently and for being dioecious. We found C. album to be hermaphroditic, C. foliosum and M. nuttalliana to be gynomonoecious, while C. bonus-henricus …

A Systems Biology Approach To Detect Eqtls Associated With Mirna And Mrna Co-Expression Networks In The Nucleus Accumbens Of Chronic Alcoholic Patients, Mohammed Mamdani

Theses and Dissertations

Alcohol Dependence (AD) is a chronic substance use disorder with moderate heritability (60%). Linkage and genome-wide association studies (GWAS) have implicated a number of loci; however, the molecular mechanisms underlying AD are unclear. Advances in systems biology allow genome-wide expression data to be integrated with genetic data to detect expression quantitative trait loci (eQTL), polymorphisms that regulate gene expression levels, influence phenotypes and are significantly enriched among validated genetic signals for many commonly studied traits including AD.

We integrated genome-wide mRNA and miRNA expression data with genotypic data from the nucleus accumbens (NAc), a major addiction-related brain region, of 36 …

Salamander Colonization Of Chase Lake, Stutsman County, North Dakota, David M. Mushet, Kyle I. Mclean, Craig A. Stockwell

The Prairie Naturalist

Salt concentrations in lakes are dynamic. In the western United States, water diversions have caused significant declines in lake levels resulting in increased salinity, placing many aquatic species at risk (Galat and Robinson 1983, Beutel et al. 2001). Severe droughts can have similar effects on salt concentrations and aquatic communities (Swanson et al. 2003). Conversely, large inputs of water can dilute salt concentrations and contribute to community shifts (Euliss et al. 2004).

Chase Lake is a large, shallow, alkaline lake in east-central North Dakota most famously known for supporting one of the largest breeding colonies of the American white pelican …

How Important Is A Quality Manuscript Review?, Christopher N. Jacques

The Prairie Naturalist

Temperatures are finally starting to cool a bit (for those of us in the northern Great Plains region) and Thanksgiving break is just around the corner.

I offer my reflections in the spirit of encouraging each of you to take a break from your professional obligations and spend time with friends and family enjoying nature and everything it has to offer this fall.