Systems Biology Commons^™

High Rates Of Hiv Seroconversion In Pregnant Women And Low Reported Levels Of Hiv Testing Among Male Partners In Southern Mozambique: Results From A Mixed Methods Study, Caroline De Schacht, Heather J. Hoffman, Nedio Mabunda, Carlota Lucas, Catharina L. Alons, Ana Madonela, Adolfo Vubil, Orlando C. Ferreira, Nurbai Calu, Iolanda S. Santos, Ilesh V. Jani, Laura Guay

Genomics and Precision Medicine Faculty Publications

Introduction

Prevention of acute HIV infections in pregnancy is required to achieve elimination of pediatric HIV. Identification and support for HIV negative pregnant women and their partners, particularly serodiscordant couples, are critical. A mixed method study done in Southern Mozambique estimated HIV incidence during pregnancy, associated risk factors and factors influencing partner's HIV testing.

Methods

Between April 2008 and November 2011, a prospective cohort of 1230 HIV negative pregnant women was followed during pregnancy. A structured questionnaire, HIV testing, and collection of dried blood spots were done at 2–3 scheduled visits. HIV incidence rates were calculated by repeat HIV testing …

A New Species And Synonymy Of The Neotropical Eucelatoria Townsend And Redescription Of Myiodoriops Townsend, Diego J. Inclán, John O. Stireman Iii

Biological Sciences Faculty Publications

The New World tropics represents the most diverse region for tachinid parasitoids (Diptera: Tachinidae), but it also contains the most narrowly defined, and possibly the most confusing, tachinid genera of any biogeographic region. This over-splitting of genera and taxonomic confusion has limited progress toward our understanding the family in this region and much work is needed to revise, redefine, and make sense of the profusion of finely split taxa. In a recent analysis of the Neotropical genus Erythromelana Townsend, two species previously assigned to this genus, Euptilodegeeria obumbrata (Wulp) and Myiodoriops marginalis Townsend were reinstated as monotypic genera. In the …

Whole Exome Sequencing In Family Trios Reveals De Novo Mutations In Pura As A Cause Of Severe Neurodevelopmental Delay And Learning Disability, David Hunt, Richard J. Leventer, Cas Simons, Ryan J. Taft, Kathryn J. Swoboda, Mary Gawne-Cain, Alex C. Magee, Perter D. Turnpenny, Diana Baralle

Genomics and Precision Medicine Faculty Publications

Background De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. Here, we report the findings in four such trios.

Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. Three of our patients were ascertained from the first 1133 children to have been investigated through this large-scale study. Case 4 was a phenotypically isolated case recruited into an undiagnosed rare disorders sequencing study.

Results Protein-altering de novo mutations in PURA …

Identification Of Cell Signaling Pathway Regulated By Micrornas In Cancer Cells Using A Systems Biological Approach, Sangbae Kim

Dissertations and Theses (Open Access)

MicroRNAs (miRNAs) are single-stranded, non-coding RNA molecules that regulate gene expression via imperfect binding of the miRNA to specific sites in the 3' untranslated region of the mRNAs. Because prediction of miRNA targets is an essential step for understanding the functional roles of miRNAs, many computational approaches have been developed to identify miRNA targets. However, identifying targets remains challenging due to the inherent limitation of current prediction approaches based on imperfect complementarity between miRNA and its target mRNAs. To overcome these current limitations, we developed a novel correlation-based approach that is sequence independence to predict functional targets of miRNAs by …

Quantitative Analysis And Imaging-Based Insights Into The Characteristics And Mechanisms Of Yeast Pattern Formation, Lin Chen

Dissertations and Theses (Open Access)

Biofilm formation is a common lifestyle adapted by bacteria and fungi in response to various environmental stresses. Bacterial and fungal biofilms adhering to medical devices convey resistance to antibiotics or biocides, causing high rates of clinical infections. Microorganisms are protected from harsh environmental conditions by reduced stress penetration through the complex biofilm architecture with distinct patterns. Although the molecular regulations of surface patterning have been well characterized in bacteria, the mechanisms underlying the complex pattern formation in eukaryotic biofilms remain unclear.

This dissertation aims to investigate the salient features of robust colony expansion in yeast biofilms and the processes driving …

The Cedar Point Experience, 40 Years Of Field Based, Experiential Learning, Jon Garbisch

Discipline-Based Education Research Group Speaker Series

The Cedar Point Experience was born in the summer of 1975. At the urging of several biology faculty UNL leased the Goodall Cedar Point Girlscout Camp and offered a broad range of field based courses exploiting the local environment as their classroom. These instructors also had a strong interest in the area as a base for their own research. Today the UNL Cedar Point Biological Station with a few additional buildings can support around 100 people with full service dining, housing, classroom and lab space.

The instructional model has remained unchanged for the past 40 years. Field based or place …

Affinity Proteomics Within Rare Diseases: A Bio‐Nmd Study For Blood Biomarkers Of Muscular Dystrophies, Brucu Ayoglu, Amina Chaouch, Hans Lochmuller, Luisa Politano, Enrico Bertini, Sebahattin Cirak, +17 Additional Authors

Genomics and Precision Medicine Faculty Publications

Despite the recent progress in the broad‐scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO‐NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven …

Development And Evaluation Of A Model For Secondary Evolution Educators’ Professional Development Needs, William L. Romine, Ellen Barnett, Patricia J. Friedrichsen, Aaron J. Sickel

Biological Sciences Faculty Publications

Background

Professional development (PD) efforts have improved acceptance and pedagogical practice related to the theory of evolution in high school biology teachers. However, these teachers express need for more PD related to evolution. It therefore becomes necessary to understand teachers’ PD needs prior to structuring PD efforts.

Methods

We formulated and validated a model to explain secondary teachers’ PD needs using data from a survey of 276 secondary biology teachers who reported teaching evolution.

Results

In addition to reliable subscales, we found that obstacles to teaching evolution, school and community support for evolution instruction, confidence in evolution instruction, and prior …

White Fringetree, Chionanthus Virginicus, As A Novel Larval Host For Emerald Ash Boer, Don Cipollini

Biological Sciences Faculty Publications

Emerald ash borer is an invasive Asian pest of ash species in North America. All North American species of ash tested so far are susceptible to it, but there are no published reports of this insect developing fully in non-ash hosts in the field in North America. I report here evidence that EAB can attack and complete development in white fringetree, Chionanthus virginicus L., a species native to the southeastern U.S. that is also planted ornamentally.

Mechanisms Of Ash Resistance To Emerald Ash Borer: Progress And Gaps, Caterina Villari, Justin G.A. Whitehill, Don Cipollini, Daniel A. Herms, Pierluigi Bonello

Biological Sciences Faculty Publications

The emerald ash borer (EAB) invasion of North America has caused widespread mortality of native ash, and is threatening the native ash resources. As a consequence of its devastating impact, EAB has caught the attention of the scientific community, and several studies have focused on different aspects of the biology and behavior of this pest, including its interaction with host defenses. Here we present a review of the published literature on mechanisms of ash resistance to EAB, the understanding of which, despite starting from a tabula rasa, has achieved significant progress in the last few years.

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. …

Aquaponics And Basil Plant Density, Danika L. Macmaster, Brook Murphy, Dudley Burton

STAR Program Research Presentations

Aquaponics is the use of water from a fish tank to provide nutrients to plants in a soil-less environment. The rocks cultivate the bacteria that turns the ammonia into nitrates that the plants need, and the plant bed functions as a filter for the fish tank. In this study, with the guidance of Doctor Dudley Burton, Doctor Brook Murphy, we researched the optimal plant density for basil in an Aquaponics system. We attempted to control or measure all the other variables to consider, as to isolate the variable of distance between plants. The water flow was spread through the plant …

Manitoba Tall Grass Prairie Preserve: Providing Habitat For Protected And Provincially Rare Species, Christie L. Borkowsky

The Prairie Naturalist

The establishment of the Manitoba Tall Grass Prairie Preserve in 1989 secured some of the largest and highest quality parcels of tall grass prairie remaining in the province. Shortly after securement by either Nature Manitoba (formerly Manitoba Naturalists Society) or Manitoba Habitat Heritage Corporation, seasonal staff from the Critical Wildlife Habitat Program (CWHP) began inventory efforts to document the various floral and faunal species occurring on these acquisitions. With the addition of the Nature Conservancy of Canada to the Preserve partnership, the Preserve has grown in size to nearly 5,000 ha. The list of species identified on the Preserve has …

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 …

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 …

Historic Distribution And Ecology Of Tall-Grass Prairie In Western Canada, Darcy C. Henderson, Nicola Koper

The Prairie Naturalist

Rapid settlement and agricultural development of western Canada in the late 1800s and early 1900s nearly eliminated the tall-grass prairie, and pre-empted a detailed description by ecologists. A combination of literature review and historical ecological analysis of soils, climate, and composition data are applied to estimate the historic distribution, and area occupied by tall-grass prairie in southern Manitoba and southeastern Saskatchewan, Canada. The resulting area estimate of 20,830 km² is more than three times any previously reported value. Some confusion of terms from the first half of the 1900s, and the impact of invasive species on vegetation patterns observed …

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 …

Soil Chemical Responses To Fire Seasonality And Frequency In A Texas Grassland, Domingo M. Jariel Jr., R. James Ansley, Betty A. Kramp, David L. Jones

The Prairie Naturalist

On a clay-loam mixed grassland dominated by honey mesquite (Prosopis glandulosa Torr.) in northern Texas, we quantified soil pH, soil organic carbon (OC), electrical conductivity (EC), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sodium (Na), zinc (Zn), iron (Fe), manganese (Mn) and copper (Cu) in response to various effects of summer and winter fire treatments from 1991–1996. We conducted summer fire between August and September, and winter fire between January and March. Treatments that included summer fires increased soil pH, EC, Na, and Cu and temporarily decreased soil OC and Mn (P ≤ 0.05). The winter fire treatment …

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 …

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 …

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. …

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 …

Prairie Restoration: Bridging The Past And The Future, Daryl D. Smith

The Prairie Naturalist

Tallgrass prairie once dominated most of mid-continent North America. Conversion of this prairie to cropland was rapid and extensive. Today, it is the most decimated ecosystem in North America with less than two percent remaining. Prairie reconstruction began at the University of Wisconsin Arboretum in the 1930s. Thirty years later, exemplary initiatives by a group of highly motivated restorationists in Illinois and Iowa became a part of the legacy of restoration ecology. Their work generated widespread public interest in prairie restoration and initiated the ongoing biennial North American Prairie Conference. Since then, practitioners have made significant advances in reconstruction and …

Reproductive Failure In Largeleaf Wild Indigo In A Restored Prairie In Southeastern Minnesota, Neal D. Mundahl

The Prairie Naturalist

Native prairie restorations in many regions of the United States have been hindered by various herbivores consuming plant reproductive parts or products. I conducted field studies of a population of largeleaf wild indigo (Baptisia lactea) on a restored prairie in southeastern Minnesota during the growing seasons of 2010–2012 to determine the cause(s) of repeated reproductive failure. I assessed plants for browsing damage caused by white-tailed deer (Odocoileus virginianus) during the period of flowering and with a deer exclosure experiment involving caged and non-caged plants. I compared reproductive output (numbers of seed pods, viable seeds) of caged …

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 …

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 …

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. …