Life Sciences Commons^™

Empirical Demonstration Of Environmental Sensing In Catalytic Rna: Evolution Of Interpretive Behavior At The Origins Of Life, Niles Lehman, Tess Bernhard, Brian C. Larson, Andrew J.N. Robinson, Christopher C.B. Southgate

Chemistry Faculty Publications and Presentations

Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically.

Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. …

Spring Thaw Ionic Pulses Boost Nutrient Availability And Microbial Growth In Entombed Antarctic Dry Valley Cryoconite Holes, Jon Telling, Alexandre M. Anesio, Martyn Tranter, Andrew G. Fountain, Thomas H. Nylen, Jon Hawkings, Virendra B. Singh, Preeti Kaur, Michaela Musilova, Jemma L. Wadham

Geology Faculty Publications and Presentations

The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During …

Antibacterial Gene Transfer Across The Tree Of Life, Jason A. Metcalf, Lisa J. Funkhouser-Jones, Kristen A. Brileya, Anna-Louise Reysenbach, Seth R. Bordenstein

Biology Faculty Publications and Presentations

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, …

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel L. Speiser, Molly S. Pankey, Alexander K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Biology Faculty Publications and Presentations

Background: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to …

Structural Insights Into The Architecture Of The Hyperthermophilic Fusellovirus Ssv1, Kenneth M. Stedman, Melissa Deyoung, Mitul Saha, Michael B. Sherman, Marc C. Morais

Biology Faculty Publications and Presentations

The structure and assembly of many icosahedral and helical viruses are well-characterized. However, the molecular basis for the unique spindle-shaped morphology of many viruses that infect Archaea remains unknown. To understand the architecture and assembly of these viruses, the spindle-shaped virus SSV1 was examined using cryo-EM, providing the first 3D-structure of a spindle-shaped virus as well as insight into SSV1 biology, assembly and evolution. Furthermore, a geometric framework underlying the distinct spindle-shaped structure is proposed.

Inhalable Constituents Of Thirdhand Tobacco Smoke: Chemical Characterization And Health Impact Considerations, Mohamad Sleiman, Jennifer M. Logue, Wentai Luo, James F. Pankow, Lara A. Gundel, Hugo Destaillats

Chemistry Faculty Publications and Presentations

Tobacco smoke residues lingering in the indoor environment, also termed thirdhand smoke (THS), can be a source of long-term exposure to harmful pollutants. THS composition is affected by chemical transformations and by air–surface partitioning over time scales of minutes to months. This study identified and quantified airborne THS pollutants available for respiratory exposure, identified potential environmental tracers, and estimated health impacts to nonsmokers. In a ventilated 18 m3 laboratory chamber, six cigarettes were machine-smoked, and levels of particulate matter (PM2.5) and 58 volatile organic compounds (VOCs) were monitored during an aging period of 18 h. Results were compared with field …

Predicted Effects Of Gypsy Moth Defoliation And Climate Change On Forest Carbon Dynamics In The New Jersey Pine Barrens, Alec M. Kretchun, Robert M. Scheller, Melissa S. Lucash, Kenneth L. Clark, John Hom, Steve Van Tuyl

Environmental Science and Management Faculty Publications and Presentations

Disturbance regimes within temperate forests can significantly impact carbon cycling. Additionally, projected climate change in combination with multiple, interacting disturbance effects may disrupt the capacity of forests to act as carbon sinks at large spatial and temporal scales. We used a spatially explicit forest succession and disturbance model, LANDIS-II, to model the effects of climate change, gypsy moth (Lymantria dispar L.) defoliation, and wildfire on the C dynamics of the forests of the New Jersey Pine Barrens over the next century. Climate scenarios were simulated using current climate conditions (baseline), as well as a high emissions scenario (HadCM3 A2 …

Associations Between Prenatal Exposure To Air Pollution, Small For Gestational Age, And Term Low Birthweight In A State-Wide Birth Cohort, Lisa C. Vinikoor-Imler, J. Allen Davis, Robert E. Meyer, Lynne C. Messer, Thomas J. Luben

Community Health Faculty Publications and Presentations

A range of health effects, including adverse pregnancy outcomes, have been associated with exposure to ambient concentrations of particulate matter (PM) and ozone (O₃). The objective of this study was to determine whether maternal exposure to fine particulate matter (PM_2.5) and O₃ during pregnancy is associated with the risk of term low birthweight and small for gestational age infants in both single and co-pollutant models. Term low birthweight and small for gestational age were determined using all birth certificates from North Carolina from 2003 to 2005. Ambient air concentrations of PM_2.5 and O_{3 …}

Report On The Workshop For Life Detection In Samples From Mars, Gerhard Kminek, Catherine Conley, Carlton C. Allen, Douglas H. Bartlett, David W. Beaty, Liane G. Benning, Rohit Bhatia, Penelope J. Boston, Caroline Duchaine, Jack D. Farmer, George J. Flynn, Daniel P. Glavin, Yuri Gorby, John E. Hallsworth, Rakesh Mogul, Duane Moser, P. Buford Price, Ruediger Pukall, David Fernandez-Remolar, Caroline L. Smith, Kenneth M. Stedman, Andrew Steele, Ramunas Stepanauskas, Henry Sun, Jorge L. Vago, Mary A. Voytek, Paul S. Weiss, Frances Westfall

Biology Faculty Publications and Presentations

The question of whether there is or was life on Mars has been one of the most pivotal since Schiaparellis’ telescopic observations of the red planet. With the advent of the space age, this question can be addressed directly by exploring the surface of Mars and by bringing samples to Earth for analysis. The latter, however, is not free of problems. Life can be found virtually everywhere on Earth. Hence the potential for contaminating the Mars samples and compromising their scientific integrity is not negligible. Conversely, if life is present in samples from Mars, this may represent a potential source …

Identification Of Novel Small Rnas And Characterization Of The 6s Rna Of Coxiella Burnetii, Indu Warrier, Linda D. Hicks, James M. Battisti, Rahul Raghavan, Michael F. Minnick

Biology Faculty Publications and Presentations

Coxiella burnetii, an obligate intracellular bacterial pathogen that causes Q fever, undergoes a biphasic developmental cycle that alternates between a metabolically-active large cell variant (LCV) and a dormant small cell variant (SCV). As such, the bacterium undoubtedly employs complex modes of regulating its lifecycle, metabolism and pathogenesis. Small RNAs (sRNAs) have been shown to play important regulatory roles in controlling metabolism and virulence in several pathogenic bacteria. We hypothesize that sRNAs are involved in regulating growth and development of C. burnetii and its infection of host cells. To address the hypothesis and identify potential sRNAs, we subjected total RNA isolated …

The Community Economic Impacts Of Large Wildfires: A Case Study From Trinity County, California, Emily Jane Davis, Cassandra Moseley, Max Nielsen-Pincus, Pamela J. Jakes

Environmental Science and Management Faculty Publications and Presentations

Wildfires are increasing in severity and frequency in the American West, but there is limited understanding of their economic effects at the community level. We conducted a case study of the impacts of large wildfires in 2008 in Trinity County, California, by examining labor market, suppression spending, and qualitative interview data. We found that the 2008 fires had interrelated effects on several economic sectors in the county. Labor market data indicated a decrease in total private-sector employment and wages and an increase in public-sector employment and wages during the summer of 2008 compared to the previous year, while interviews captured …

Candy Flavorings In Tobacco, Jessica E. Brown, Wentai Luo, Lorne M. Isabelle, James F. Pankow

Chemistry Faculty Publications and Presentations

Professor James F. Pankow reveals striking similarities between the patterns in the flavoring chemicals used in flavored tobacco products and those in popular candy and Kool-Aid products. The authors analyzed 12 artificially flavored candy and fruit drink products and compared them to 15 widely-available flavored tobacco products. They found significant overlap in the chemical signatures of the flavor chemicals. Several of the tobacco products contained flavor chemicals at much higher concentrations than in the non-tobacco products.

Variation In Sex Allocation And Floral Morphology In An Expanding Distylous Plant Hybrid Complex, Jennifer Rhode Ward, M. Leigh Cowart, Julie Clifford, Mieko Camp, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Premise of research. Sex allocation, the relative energy devoted to producing pollen, ovules, and floral displays, can significantly affect reproductive output and population dynamics. In this study, we investigated floral morphology and gamete production in bisexual, distylous plants from a self-incompatible hybrid complex (Piriqueta cistoides ssp. caroliniana Walter [Arbo]; Turneraceae). Sampling focused on two parent types (C, V) and their stable hybrid derivative (H). Since H morphotypes are heterotic for growth and fruit production, we hypothesized that they would produce larger flowers with more gametes. We also anticipated that plants with long styles (long morphs) would produce less …

Assessing The Homogenization Of Urban Land Management With An Application To Us Residential Lawn Care, Colin Polsky, J. Morgan Grove, Chris Knudson, Peter M. Groffman, Neil D. Bettez, Jeannine Cavender-Bares, Sharon J. Hall, James B. Heffernan, Sarah E. Hobbie, Kelli L. Larson, Jennifer L. Morse, Christopher Neill, Kristen C. Nelson, Laura A. Ogden, Jarlath O'Neil-Dunne, Diane E. Pataki, Rinku Roy Chowdhury, Meredith K. Steele

Environmental Science and Management Faculty Publications and Presentations

Changes in land use, land cover, and land management present some of the greatest potential global environmental challenges of the 21st century. Urbanization, one of the principal drivers of these transformations, is commonly thought to be generating land changes that are increasingly similar. An implication of this multiscale homogenization hypothesis is that the ecosystem structure and function and human behaviors associated with urbanization should be more similar in certain kinds of urbanized locations across biogeophysical gradients than across urbanization gradients in places with similar biogeophysical characteristics. This paper introduces an analytical framework for testing this hypothesis, and applies the framework …

Levels Of Altruism, Martin Zwick, Jeffrey Alan Fletcher

Systems Science Faculty Publications and Presentations

The phenomenon of altruism extends from the biological realm to the human socio-cultural realm. This paper sketches a coherent outline of multiple types of altruism of progressively increasing scope that span these two realms and are grounded in an ever-expanding sense of"self." Discussion of this framework notes difficulties associated with altruisms at different levels. It links scientific ideas about the evolution of cooperation and about hierarchical order to perennial philosophical and religious concerns. It offers a conceptual background for inquiry into societal challenges that call for altruistic behavior, especially the challenge of environmental and social sustainability.

Riparian Vegetation Assemblages And Associated Landscape Factors Across An Urbanizing Metropolitan Area, Christa Von Behren, Andrew Evans Dietrich, J. Alan Yeakley

Environmental Science and Management Faculty Publications and Presentations

While diverse, native riparian vegetation provides important functions, it remains unclear to what extent these assemblages can persist in urban areas, and under what conditions. We characterized forested riparian vegetation communities across an urbanizing metropolitan area and examined their relationships with surrounding land cover. We hypothesized that native and hydrophilic species assemblages would correlate with forest cover in the landscape. For each of 30 sites in the Portland–Vancouver metro area, we recorded vegetation at 1-cm intervals along 3 transects using the line-intercept method. Land cover was characterized at 2 scales: within 500 m of each site and across the entire …

Climate Change Effects On Northern Great Lake (Usa) Forests: A Case For Preserving Diversity, Matthew Joshua Duveneck, Robert M. Scheller, Mark A. White, Stephen D. Handler, Catherine Ravenscroft

Environmental Science and Management Faculty Publications and Presentations

Under business as usual (BAU) management, stresses posed by climate change may exceed the ability of Great Lake forests to adapt. Temperature and precipitation projections in the Great Lakes region are expected to change forest tree species composition and productivity. It is unknown how a change in productivity and/or tree species diversity due to climate change will affect the relationship between diversity and productivity. We assessed how forests in two landscapes (i.e., northern lower Michigan and northeastern Minnesota, USA) would respond to climate change and explored the diversityproductivity relationship under climate change. In addition, we explored how tree species diversity …

Archaeological Data Provide Alternative Hypotheses On Pacific Herring (Clupea Pallasii) Distribution, Abundance, And Variability, Iain Mckechnie, Dana Lepofsky, Madonna L. Moss, Virginia L. Butler, Trevor J. Orchard, Gary Coupland, Frederick Foster, Megan Caldwell, Ken Lertzman

Anthropology Faculty Publications and Presentations

Over the last century, Pacific herring, a forage fish of tremendous cultural, economic, and ecological importance, has declined in abundance over much of its range. We synthesize archaeological fisheries data spanning the past 10,000 y from Puget Sound in Washington to southeast Alaska to extend the ecological baseline for herring and contextualize the dynamics of modern industrial fisheries. While modern herring populations can be erratic and exhibit catastrophic declines, the archaeological record indicates a pattern of consistent abundance, providing an example of long-term sustainability and resilience in a fishery known for its modern variability. The most parsimonious explanation for the …

Structural Dynamics Of A Mitochondrial Trna Possessing Weak Thermodynamic Stability, Hari Bhaskaran, Takaaki Taniguchi, Takeo Suzuki, Tsutomu Suzuki, John J. Perona

Chemistry Faculty Publications and Presentations

Folding dynamics are ubiquitously involved in controlling the multivariate functions of RNAs. While the high thermodynamic stabilities of some RNAs favor purely native states at equilibrium, it is unclear whether weakly stable RNAs exist in random, partially folded states or sample well-defined, globally folded conformations. Using a folding assay that precisely tracks the formation of native aminoacylable tRNA, we show that the folding of a weakly stable human mitochondrial (hmt) leucine tRNA is hierarchical with a distinct kinetic folding intermediate. The stabilities of the native and intermediate conformers are separated by only about 1.2 kcal/mol, and the species are readily …

The Design And Use Of Forest Decision Support Systems In The Usa, Sean N. Gordon, Keith M. Reynolds

Institute for Sustainable Solutions Publications and Presentations

Computer-based tools for supporting forest management. The experience and the expertise world-wide answers a call from both the research and the professional communities for a synthesis of current knowledge about the use of computerized tools in forest management planning. According to the aims of the Forest Management Decision Support Systems (FORSYS) (http://fp0804.emu.ee/) this synthesis is a critical success factor to develop a comprehensive quality reference for forest management decision support systems.

The emphasis of the book is on identifying and assessing the support provided by computerized tools to enhance forest management planning in real-world contexts. The book thus identifies the …

Getting Plant Conservation Right (Or Not): The Case Of The United States, Kayri Havens, Andrea T. Kramer, Edward O. Guerrant Jr.

Environmental Science and Management Faculty Publications and Presentations

Effective plant conservation includes addressing basic needs such as information about species distribution and rarity; research, management, education, and training capacity to mitigate threats facing threatened species; policy and funding to support continued capacity and conservation; and, ultimately, a public that understands and supports the importance of plants and the need for their conservation. Coordination of plant conservation efforts is also needed to ensure that resources and expertise are used in a strategic, efficient, and effective manner.We argue that no country is currently getting plant conservation right; plants are becoming increasingly rare around the world. Plants are often not fully …

Endogenous Ros Levels In C. Elegans Under Exogenous Stress Support Revision Of Oxidative Stress Theory Of Life-History Tradeoffs, Samson W. Smith, Leigh C. Latta Iv, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals.

Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with …

Small Tidal Channels Improve Foraging Opportunities For Calidris Shorebirds, Aileen K. Miller, Catherine E. De Rivera

Environmental Science and Management Faculty Publications and Presentations

Estuarine intertidal habitats are heterogeneous, therefore migratory shorebirds are expected to forage in microhabitats where they can maximize their energy intake. Identifying proximate factors that migratory shorebirds use to accept or reject a particular habitat patch will help land managers make conservation and restoration decisions that provide the greatest benefits to shorebird populations during migration, a period of intense energy usage. We examined whether small semipermanent tidal channels were preferentially used by foraging Western Sandpipers (Calidris mauri) and Dunlins (C. alpina) during a spring migratory stopover in Bandon Marsh, an Oregon, USA, estuary. Further, we tested …

Multimodel Simulations Of Forest Harvesting Effects On Long-Term Productivity And Cn Cycling In Aspen Forests, Fugui Wang, David J. Mladenoff, Jodi A. Forrester, Juan A. Blanco, Robert M. Scheller, Scott D. Peckham, Cindy Keough, Melissa S. Lucash

Environmental Science and Management Faculty Publications and Presentations

The effects of forest management on soil carbon (C) and nitrogen (N) dynamics vary by harvest type and species. We simulated long-term effects of bole-only harvesting of aspen (Populus tremuloides) on stand productivity and interaction of CN cycles with a multiple model approach. Five models, Biome-BGC, CENTURY, FORECAST, LANDIS-II with Century-based soil dynamics, and PnET-CN, were run for 350 years with seven harvesting events on nutrient-poor, sandy soils representing northwestern Wisconsin, USA. Twenty CN state and flux variables were summarized from the models' outputs, and statistically analyzed using ordination and variance analysis methods. The multiple models' averages suggest that bole-only …

Novel Cul3 Binding Proteins Function To Remodel E3 Ligase Complexes, Wananit Wimuttisuk, Mark West, Brittney Davidge, Kebing Yu, Arthur Salomon, Jeffrey D. Singer

Biology Faculty Publications and Presentations

Background: Cullins belong to a family of scaffold proteins that assemble multi-subunit ubiquitin ligase complexes to recruit protein substrates for ubiquitination via unique sets of substrate adaptor, such as Skp1 or Elongin B, and a substrate-binding protein with a conserved protein-protein interacting domain, such as leucine-rich repeats (LRR), a WD40 domain, or a zinc-finger domain. In the case of the Cullin3 (Cul3), it forms a BTB-Cul3-Rbx1 (BCR) ubiquitin ligase complex where it is believed that a BTB domain-containing protein performs dual functions where it serves as both the substrate adaptor and …

Experimental Analysis Of Nest-Site Choice And Its Relationship To Nest Success In An Open-Cup–Nesting Passerine, Sarah Cancellieri, Michael T. Murphy

Biology Faculty Publications and Presentations

Nest placement presumably reflects selection for secure sites to minimize failure. Most tests of this hypothesis, however, have failed to support it. We used artificial nests (ARTs) to experimentally evaluate nest-site-choice behavior by an open-cup–nesting bird, the Eastern Kingbird (Tyrannus tyrannus). In 2010 and 2011, we placed ARTs in trees in the riparian zone at Malheur National Wildlife Refuge, Oregon, USA, to test whether (1) characteristics describing the physical location in trees of used and unused ARTs differed, (2) used ART sites more closely resembled naturally chosen sites, (3) successful natural nests (NATs) and successful ARTs were similarly …

Report And Recommendations Of The Balance Of Crop Research Working Group Of The National Agricultural Research, Extension, Education And Economics (Nareee) Advisory Board, Mark Mclellan, Leo Holt, Twilya L'Ecuyer, Robert Taylor, Julia Sabin, Milo Shult, Anne Marie Thro, Paul Heisey

Biology Faculty Publications and Presentations

In December of 2012, the President’s Council of Advisors on Science & Technology (PCAST) issued a report to the President on Agricultural Preparedness and the Agriculture Research Enterprise. The PCAST report recognizes the long-term history of public investment in agricultural research. The report also recognized significant private investment into agricultural research. Significantly, the report is adamant that the agricultural research enterprise is not prepared to meet the challenges of the 21st century. The report cited two reasons:

1. too little competitive research and
2. an imbalance of research priorities between private and public funding sources.

This report addresses the latter issue.

Members …

Sampling For Effective Ex Situ Plant Conservation, Edward O. Guerrant Jr., Kayri Havens, Pati Vitt

Environmental Science and Management Faculty Publications and Presentations

Sampling a whole flora or any significant subset for ex situ conservation purposes is a complex, long-term proposition. Thus, it is important to consider what constitutes an adequate sample not only for all taxa as a whole but also for each taxon individually as well as how to strategically schedule collection over time. There are five basic sampling questions: from which species to collect, from how many and which populations, from how many and which individuals, how many and what kind of propagules to collect, and, finally, at what point is the desired sample size too great for a population …

Impacts Of Fire And Climate Change On Long-Term Nitrogen Availability And Forest Productivity In The New Jersey Pine Barrens, Melissa S. Lucash, Robert M. Scheller, Alec M. Kretchun, Kenneth L. Clark, John Hom

Environmental Science and Management Faculty Publications and Presentations

Increased wildfires and temperatures due to climate change are expected to have profound effects on forest productivity and nitrogen (N) cycling. Forecasts about how wildfire and climate change will affect forests seldom consider N availability, which may limit forest response to climate change, particularly in fire-prone landscapes. The overall objective of this study was to examine how wildfire and climate change affect long-term mineral N availability in a fire-prone landscape. We employed a commonly used landscape simulation model (LANDIS-II) in the New Jersey Pine Barrens, a landscape characterized by frequent small fires and fire-resilient vegetation. We found that fire had …