Life Sciences Commons^™

(Non)Parallel Developmental Mechanisms In Vertebrate Appendage Reduction And Loss, Samantha Swank, Thomas Sanger, Yoel E. Stuart

Biology: Faculty Publications and Other Works

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. …

Microplastic In Riverine Fish Is Connected To Species Traits, R. E. Mcneish, L. H. Kim, H. A. Barrett, S. A. Mason, J. J. Kelly, T. J. Hoellein

Biology: Faculty Publications and Other Works

Microplastic is a contaminant of concern worldwide. Rivers are implicated as major pathways of microplastic transport to marine and lake ecosystems, and microplastic ingestion by freshwater biota is a risk associated with microplastic contamination, but there is little research on microplastic ecology within freshwater ecosystems. Microplastic uptake by fish is likely affected by environmental microplastic abundance and aspects of fish ecology, but these relationships have rarely been addressed. We measured the abundance and composition of microplastic in fish and surface waters from 3 major tributaries of Lake Michigan, USA. Microplastic was detected in fish and surface waters from all 3 …

Harvesting Invasive Plants To Reduce Nutrient Loads And Produce Bioenergy: An Assessment Of Great Lakes Coastal Wetlands, Brendan D. Carson, Shane C. Lishawa, Nancy C. Tuchman, Andrew M. Monks, Beth A. Lawrence, Dennis A. Albert

School of Environmental Sustainability: Faculty Publications and Other Works

In Laurentian Great Lakes coastal wetlands (GLCWs), dominant emergent invasive plants are expanding their ranges and compromising the unique habitat and ecosystem service values that these ecosystems provide. Herbiciding and burning to control invasive plants have not been effective in part because neither strategy addresses the most common root cause of invasion, nutrient enrichment. Mechanical harvesting is an alternative approach that removes tissue‐bound phosphorus and nitrogen and can increase wetland plant diversity and aquatic connectivity between wetland and lacustrine systems. In this study, we used data from three years of Great Lakes‐wide wetland plant surveys, published literature, and bioenergy analyses …

New Genera And Species Of Fossil Marine Amioid Fishes (Actinopterygii, Holostei) From The Late Cretaceous Agoult Locality In Southeastern Morocco, Mark V. Wilson, Alison M. Murray, Terry C. Grande

Biology: Faculty Publications and Other Works

The document is Terry C. Grande's (et al.) abstract in the Society of Vertebrate Paleontology 77th Annual Meeting Program and Abstracts.

Ecological Restoration, Elizabeth P. Mccann, Tania Schusler

School of Environmental Sustainability: Faculty Publications and Other Works

Ecological restoration involves revitalizing neglected, degraded, damaged, or destroyed habitats.

• Restoration-based education involves learners in ecological restoration with an intentional educational purpose.

• Urban restoration-based education can enhance personal and community well-being while improving ecosystem services in degraded environments.

• Restoration-based education can benefit from consciously forming partner ships, integrating local values alongside socioeconomic and ecological considerations, and being sensitive to issues of power and diverse cultures.

Mechanical Harvesting Effectively Controls Young Typha Spp. Invasion And Unmanned Aerial Vehicle Data Enhances Post-Treatment Monitoring, Shane Lishawa, Brendan D. Carson, Jodi S. Brandt, Jason M. Tallant, Nicholas J. Reo, Dennis A. Albert, Andrew M. Monks, Joseph M. Lautenbach

School of Environmental Sustainability: Faculty Publications and Other Works

The ecological impacts of invasive plants increase dramatically with time since invasion. Targeting young populations for treatment is therefore an economically and ecologically effective management approach, especially when linked to post-treatment monitoring to evaluate the efficacy of management. However, collecting detailed field-based post-treatment data is prohibitively expensive, typically resulting in inadequate documentation of the ecological effects of invasive plant management. Alternative approaches, such as remote detection with unmanned aerial vehicles (UAV), provide an opportunity to advance the science and practice of restoration ecology. In this study, we sought to determine the plant community response to different mechanical removal treatments to …

Freshwater Metaviromics And Bacteriophages: A Current Assessment Of The State Of The Art In Relation To Bioinformatic Challenges, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with …

18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti

Bioinformatics Faculty Publications

Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Bioinformatics Faculty Publications

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Bioinformatics Faculty Publications

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

Acute Effects Of Tio2 Nanomaterials On The Viability And Taxonomic Composition Of Aquatic Bacterial Communities Assessed Via High-Throughput Screening And Next Generation Sequencing, Binh Chu, Tiezheng Tong, Jean-François Gaillard, Kimberley A. Gray, John J. Kelly

Biology: Faculty Publications and Other Works

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of …

Anthropogenic Litter In Urban Freshwater Ecosystems: Distribution And Microbial Interactions, Timothy Hoellein, Miguel Rojas, Adam Pink, Joseph Gasior, John J. Kelly

Biology: Faculty Publications and Other Works

Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously …

Temporal Variations In The Abundance And Composition Of Biofilm Communities Colonizing Drinking Water Distribution Pipes, John J. Kelly, Nicole Minalt, Alessandro Culotti, Marsha Pryor, Aaron Packman

Biology: Faculty Publications and Other Works

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities …

Advancing Synthetic Ecology: Database System To Facilitate Complex Ecological Meta-Analyses, V. Bala Chaudhary

School of Environmental Sustainability: Faculty Publications and Other Works

No abstract provided.

Sustainability Education As A Catalyst For University And Community Partnerships, Shane Lishawa, Adam Schubel, Alison Varty, Nancy Tuchman

School of Environmental Sustainability: Faculty Publications and Other Works

Universities are uniquely positioned to lead society toward sustainability and their collaborations with community organizations are essential to this transition. The Biodiesel Program at Loyola University Chicago Center for Urban Environmental Research and Policy provides a case study of course-based service-learning projects facilitating synergies between the university and the community while concomitantly fostering urban sustainability. This article discusses the program’s design andstructure, and describes specific examples of community partnerships that havebenefited the university, the community, and the environment

Mysterious Mycorrhizae? A Field Trip And Classroom Experiment To Demystify The Symbioses Formed Between Plants And Fungi, Nancy C. Johnson, V. Bala Chaudhary, Jason D. Hoeksema, John C. Moore, Anne Pringle

School of Environmental Sustainability: Faculty Publications and Other Works

No abstract provided.

Untangling The Biological Contributions To Soil Stability In Semiarid Shrublands, V. Bala Chaudhary, Matthew A. Bowker, Thomas E. O'Dell, James B. Grace, Andrea E. Redman, Mathias C. Rillig, Nancy C. Johnson

School of Environmental Sustainability: Faculty Publications and Other Works

Communities of plants, biological soil crusts (BSCs), and arbuscular mycorrhizal (AM) fungi are known to influence soil stability individually, but their relative contributions, interactions, and combined effects are not well understood, particularly in arid and semiarid ecosystems. In a landscape-scale field study we quantified plant, BSC, and AM fungal communities at 216 locations along a gradient of soil stability levels in southern Utah, USA. We used multivariate modeling to examine the relative influences of plants, BSCs, and AM fungi on surface and subsurface stability in a semiarid shrubland landscape. Models were found to be congruent with the data and explained …