Systems Biology Commons^™

Asynchronous Remodeling Is A Driver Of Failed Regeneration In Duchenne Muscular Dystrophy, Sherry Dadgar, Zuyi Wang, Helen Johnston, Akanchha Kesari, Kanneboyina Nagaraju, Yi-Wen Chen, D. Ashley Hill, Terence A. Partridge, Robert J. Freishtat, Javad Nazarian, Jianhua Xuan, Yue Wang, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

We sought to determine the mechanisms underlying failure of muscle regeneration that is observed in dystrophic muscle through hypothesis generation using muscle profiling data (human dystrophy and murine regeneration). We found that transforming growth factor β-centered networks strongly associated with pathological fibrosis and failed regeneration were also induced during normal regeneration but at distinct time points. We hypothesized that asynchronously regenerating microenvironments are an underlying driver of fibrosis and failed regeneration. We validated this hypothesis using an experimental model of focal asynchronous bouts of muscle regeneration in wild-type (WT) mice. A chronic inflammatory state and reduced mitochondrial oxidative capacity are …

Spatial Variation In Carbon And Nitrogen In Cultivated Soils In Henan Province, China: Potential Effect On Crop Yield, Xuelin Zhang, Qun Wang, Frank S. Gilliam, Yilun Wang, Feina Cha, Chaohai Li

Biological Sciences Faculty Research

Improved management of soil carbon (C) and nitrogen (N) storage in agro-ecosystems represents an important strategy for ensuring food security and sustainable agricultural development in China. Accurate estimates of the distribution of soil C and N stores and their relationship to crop yield are crucial to developing appropriate cropland management policies. The current study examined the spatial variation of soil organic C (SOC), total soil N (TSN), and associated variables in the surface layer (0–40 cm) of soils from intensive agricultural systems in 19 counties within Henan Province, China, and compared these patterns with crop yield. Mean soil C and …

Predation Risk, Elk, And Aspen: Comment, Robert L. Beschta, Cristina Eisenberg, John W. Laundre, William J. Ripple, Thomas P. Rooney

Biological Sciences Faculty Publications

No abstract provided.

Rapid Identification Of A Novel Complex I Mt-Nd2 M.10134c>A Mutation In A Leigh Syndrome Patient, David K. Miller, Minal J. Menezes, Cas Simons, Lisa G. Riley, Sandra T. Cooper, Sean M. Grimmond, David R. Thorburn, John Christodoulou, Ryan J. Taft

Genomics and Precision Medicine Faculty Publications

Leigh syndrome (LS) is a rare progressive multi-system neurodegenerative disorder, the genetics of which is frequently difficult to resolve. Rapid determination of the genetic etiology of LS in a 5-year-old girl facilitated inclusion in Edison Pharmaceutical’s phase 2B clinical trial of EPI-743. SNP-arrays and high-coverage whole exome sequencing were performed on the proband, both parents and three unaffected siblings. Subsequent multi-tissue targeted high-depth mitochondrial sequencing was performed using custom long-range PCR amplicons. Tissue-specific mutant load was also assessed by qPCR. Complex I was interrogated by spectrophotometric enzyme assays and Western Blot. No putatively causal mutations were identified in nuclear-encoded genes. …

Legacy Effects In Prairie Restoration: A 73-Year Spatial History, Thomas D. Brock

The Prairie Naturalist

Black Earth Rettenmund Prairie State Natural Area, one of the highest quality prairie remnants in southern Wisconsin’s Driftless Area, has been the target of extensive restoration efforts since it was acquired by the Nature Conservancy (TNC) in 1986. In the present work, I analyzed the spatial history of this prairie using a Geographical Information System (GIS) and an extended series of air photos, on-the-ground surveys, early maps, and land-use records. In 1937, when the first air photo was taken, the site was nearly devoid of trees and shrubs. In subsequent years, the site became progressively woody until at the time …

The Significance Of Micro-Prairie Reconstruction In Urban Environments, Bruno Borsari, Neal Mundahl, Malcom F. Vidrine, Marc Pastorek

The Prairie Naturalist

An aggressive urban sprawl during the last half century has not only contributed to habitat disturbance and extirpation, as well as a loss of knowledge and appreciation for biodiversity. Across the United States, prairie reconstruction has been a very effective approach for developing sustainable landscape designs in city parks and other open spaces. The purpose of this work is to focus on restoration and reconstruction of selected micro-prairies as a vehicle for enhanced place-based education and to partially remediate the consequences of global climate change and loss of pollinators. From the coastal prairies of southwestern Louisiana, to the eastern edge …

A Floristic Survey Of Selected Sites In The Loup River Valley, Nance County, Nebraska, Diane M. Flynn, Steven J. Rothenberger

The Prairie Naturalist

The Loup River Valley of Nebraska contains natural, undisturbed wet meadows with significant plant diversity. Even though these sites are infrequent and are often intermixed with heavily grazed pastures or cultivated fields, they support numerous plant and animal species that do not occur elsewhere. We surveyed three study sites (an ungrazed wet meadow; a grazed wet meadow; and a riparian area) that totaled approximately 68.8 ha during the 2010 and 2011 growing seasons. We compiled an annotated vascular plants checklist for the study area that included 244 plant species of which about 49% (119) were new county records. The mean …

Venturing Through The Tall Grass: Experiencing The Manitoba Tall Grass Prairie Preserve, Christie L. Borkowsky, Erin Zahradka

The Prairie Naturalist

The Manitoba Tall Grass Prairie Preserve (hereafter the Preserve) was established in 1989 with a goal of protecting a vanishing habitat and to educate the general public of the importance of native grasslands (M. Latta, Nature Manitoba, personal communication). Starting in the early 1990s, an annual Prairie Day event was organized in early August to provide a means of interaction between prairie enthusiasts, the general public and local residents. Self-guiding interpretive trails with rustic amenities were established in 1996 and 2004. School programs, tours, and a simple two-page newsletter have been used to promote the Preserve and bring out visitors …

Association Of Soil Conditions And Grass Species With Variable Cover Of Leafy Spurge, Terence P. Mcgonigle, Jeremy L. Timmer

The Prairie Naturalist

Variation in soil conditions and grass cover was assessed across a range of leafy spurge (Euphorbia esula L.) cover values on a sandy rangeland in Manitoba, Canada. Soil conditions varied by site but not in relation to cover of leafy spurge. We observed a significant negative relationship between total grass cover and increasing cover of leafy spurge. Only porcupine grass (Hesperostipa spartea [Trin.] Barkworth) had a negative relationship with leafy spurge, falling from high cover at low weed occurrence to only trace levels at the highest leafy spurge abundance. Neither prairie Junegrass (Koeleria macrantha [Ledeb.] Schult.), rough …

Introduction—23rd North American Prairie Conference, Dr. Douglas J. Cattani, Dr. Nicola Koper, Dr. Pamela Rutherford, Dr. Richard K. Baydack

The Prairie Naturalist

Building upon the tradition started in Illinois by Peter Schramm in 1970, with the first conference on prairies and prairie restoration, the North American Prairie Conference (NAPC) has developed a tradition of excellence in native prairie research, conservation, education and restoration of one of the worlds’ most productive, yet most endangered, ecosystems. It has spawned great interest, enthusiasm and efforts to better understand, appreciate, manage and conserve this vital part of North America’s natural and cultural history.

In early August 2012, the University of Manitoba in Winnipeg hosted the 23rd NAPC. The theme of the 2012 conference was “Celebrating Our …

Response Of Grassland Songbirds To Grazing System Type And Range Condition, Stephen K. Davis, Brenda C. Dale, Tom Harrison, David C. Duncan

The Prairie Naturalist

Much of the remaining prairie in Canada is grazed by cattle and most grassland birds of conservation concern occupy such habitat. Identifying vegetation features related to grassland bird habitat selection that can be easily understood and measured by professional range managers and livestock producers on private lands is an important step towards conserving and restoring remaining grasslands. We conducted grassland bird surveys on 28 native mixed-grass prairie pastures in southern Saskatchewan to determine whether grazing system type (season-long vs. rotational) influenced avian abundance. Grazing system had no influence on abundance of grassland passerines. Conservation agencies that promote particular grazing systems …

Potential Impacts Of Bison Wallows On A Restored Tallgrass Prairie Community, Kimran Miller, Johanna Foster, Kristen Nielsen, Mary O'Loughlin

The Prairie Naturalist

When bison (Bos bison) repeatedly roll on the ground, they denude vegetation and create wallows (semi-permanent bare areas) that alter the native prairie plant community. Responses to these wallow-related disturbances are not as well documented in restored prairies. From 1 June to 1 September 2010 and from 3 June to 6 August 2011, we examined potential responses at Neal Smith National Wildlife Refuge, a restored prairie with resident bison. We hypothesized that plants and beetles would vary along a disturbance gradient. Our predictions were: (1) near wallows, plants with weedy lifestyles would have highest cover and biomass compared …

Project Prairie And Tallgrass Education On The Rice Lake Plains: A Journey From 1870 To Today And Beyond, Todd Farrell, Mark Rupke, Mark Stabb

The Prairie Naturalist

Project Prairie began in 2011 as a curriculum-linked integrated environmental studies program to showcase the Rice Lake Plains (RLP), a tallgrass prairie landscape of sandy rolling hills located at the eastern extent of the Oak Ridges Moraine in southern Ontario. Project Prairie provides educators both indoor and outdoor activities that support their curriculum and share the story of the RLP. Project Prairie provides teacher and student resources that focus on the RLP from the mid-nineteenth century to present day. Learning objectives of Project Prairie are developed from the subjects of science, social science, language arts, geography, history, and Aboriginal culture. …

Notes: Oriental Bittersweet In Grasslands Near Eastern Bluebird Nest Boxes, Neal D. Mundahl

The Prairie Naturalist

Oriental bittersweet (Celastrus orbiculatus Thunb.; hereafter OB) is an invasive, woody vine that has been expanding its range westward in North America since its introduction from East Asia in the mid-1700s for horticultural purposes (Albright et al. 2009, United States Department of Agriculture [USDA] 2012). Although typically a woodland problem in the United States (McNab and Meeker 1987), OB can invade grassland habitats (Fike and Niering 1999), likely sprouting from seeds dropped by birds and mammals (McNab and Meeker 1987, Greenberg et al. 2001, Sarver et al. 2008) and often developing into large, shrub-like tangles of intertwining stems (Fike …

Effects Of Compost On Prairie Seedling Establishment And Seed Production, Thomas R. Rosburg, Emiy Sibigtroth, Adam Palmer

The Prairie Naturalist

Compost is a commonly used soil amendment in horticultural and agricultural practices that is generally known to improve soil conditions and plant growth. We conducted a field experiment to investigate the application of compost to prairie production plots as a method to improve seedling establishment and growth and the seed production of established plants. We evaluated the effect of compost depth and tillage on the survivorship, growth, reproduction and ecophysiology of several prairie plant species commonly used in restoration. Results were mixed; for some species, transplants in compost–amended plots incurred lower survivorship and reduced growth compared to control plots. When …

Comparative Proteomics Reveals Core Vs. Unique Molecular Signatures For Dissimilatory Metal Reducing Bacteria Grown With Various Electron Acceptors, Xiaoxin Liu

Doctoral Dissertations

Dissimilatory metal reducing bacteria (DMRB) are probably one of the most respiratory versatile microorganisms on earth. Their ability to use metals as terminal electron acceptor allows them to survive in severe environments (e.g. radionuclide contaminated soil). In addition to metals, many other organic and inorganic substrates can be utilized as electron acceptors for DMRB respiration, including fumarate, nitrate, oxygen, etc. Genome information for many DMRB species is available, which reveals large numbers of c-type cytochrome encoding genes present in their genomes. For example, the genomes of three DMRBs, Anaeromyxobacter dehalogenans strain 2CP-C, Shewanella oneidensis strain MR-1, and Geobacter daltonii …

Development Of An Experimental And Computational Platform For Enhanced Characterization Of Modified Peptides And Proteins In Environmental Proteomics, Ritin Sharma

Doctoral Dissertations

Over the last decade, mass spectrometry based proteomics has been established as the front-runner in systems-level protein expression studies. However, with the field progressing into research of more and more complex samples, novel challenges have been raised with respect to efficient protein extraction and computational matching. In this dissertation, various aspects in the proteomics workflow, including experimental and computational approaches, have been developed, optimized and systematically evaluated. In this work, some of the critical factors with respect to proteomics sample preparation, like available biomass, detergent removal methods, and intact protein fractionation to achieve deeper proteome measurements were evaluated. The presented …

Quantitative Characterization Of Proteins And Post-Translational Modifications In Complex Proteomes Using High-Resolution Mass Spectrometry-Based Proteomics, Zhou Li

Doctoral Dissertations

Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing …

Application Of A Bioenergetics Framework For Assessing Sub-Lethal Effects Of Pollutants In The Freshwater Mussel Elliptio Complanata, Christopher G. Goodchild

All Theses And Dissertations

Although biomarkers are frequently used to assess sublethal effects of contaminants, a lack of mechanistic linkages to higher-level effects limits the predictive power of biomarkers. Bioenergetics has been proposed as a framework for linking cellular effects to whole-animal effects. We investigated sublethal effects of exposure to wastewater treatment facility effluent in freshwater mussels in situ, thereby capturing ecologically relevant exposure conditions. Our study focused on the energetic biomarker AMP-activated protein kinase (AMPK), while also considering more traditional biomarkers like heat shock proteins (HSP70), and antioxidant enzymes (i.e., superoxide dismutase (SOD), glutathione-S-transferase (GST)). We examined biomarkers at mRNA and protein levels. …

Eccentric Muscle Challenge Shows Osteopontin Polymorphism Modulation Of Muscle Damage., Whitney L. Barfield, Kitipong Uaesoontrachoon, Chung-Sheih Wu, Stephen Lin, Yue Chen, Paul C. Wang, Yasmine Kanaan, Vernon Bond, Eric P. Hoffman

Genomics and Precision Medicine Faculty Publications

A promoter polymorphism of the osteopontin (OPN) gene (rs28357094) has been associated with multiple inflammatory states, severity of Duchenne muscular dystrophy (DMD) and muscle size in healthy young adults. We sought to define the mechanism of action of the polymorphism, using allele-specific in vitroreporter assays in muscle cells, and a genotype-stratified intervention in healthy controls. In vitro reporter constructs showed the G allele to respond to estrogen treatment, whereas the T allele showed no transcriptional response. Young adult volunteers (n = 187) were enrolled into a baseline study, and subjects with specific rs28357094 genotypes enrolled into an eccentric …