Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Portland State University

2012

Discipline
Keyword
Publication
Publication Type

Articles 1 - 30 of 58

Full-Text Articles in Life Sciences

Stream-Associated Amphibian Habitat Assessment In The Portland-Vancouver Metropolitan Region, Andrew Evans Dietrich Dec 2012

Stream-Associated Amphibian Habitat Assessment In The Portland-Vancouver Metropolitan Region, Andrew Evans Dietrich

Dissertations and Theses

This study assessed the influence of landscape development on stream-associated amphibians in forested riparian areas within the Portland-Vancouver metropolitan region. Human alteration of landscapes may dramatically affect the ecology of neighboring aquatic systems. It was hypothesized that lotic amphibians would be negatively associated with greater amounts of landscape development and positively associated with forested area within the surrounding watershed. Thirty-seven 1st-3rd order streams were sampled between June 21st and September 21st in 2011. Streams potentially providing adequate habitat for stream-obligate amphibians were randomly selected. Amphibians were surveyed along 30-meter stream transects using an active-cover search (ACS). Environmental variables associated with …


The Influence Of Market Proximity On National Forest Hazardous Fuels Treatments, Max Nielsen-Pincus, Susan Charnley, Cassandra Moseley Dec 2012

The Influence Of Market Proximity On National Forest Hazardous Fuels Treatments, Max Nielsen-Pincus, Susan Charnley, Cassandra Moseley

Environmental Science and Management Faculty Publications and Presentations

The US Department of Agriculture Forest Service's focus on hazardous fuels reduction has increased since the adoption of the National Fire Plan in 2001. However, appropriations for hazardous fuels reduction still lag behind wildfire suppression spending. Offsetting fuels treatment costs through biomass utilization or by using innovative administrative mechanisms such as stewardship contracting are two approaches to stretching appropriated dollars further across the landscape. We use fuels treatment data (n = 8,451 locations) to ask how wood- processing infrastructure influences where and how much hazardous fuels treatments, biomass utilization, and stewardship contracting occur on national forests in Oregon and Washington. …


Long-Term Integrated Studies Show Complex And Surprising Effects Of Climate Change In The Northern Hardwood Forest, Peter M. Groffman, Lindsay E. Rustad, Pamela H. Templer, John L. Campbell, Lynn M. Christenson, Nina K. Lany, Anne M. Socci, Matthew A. Vadeboncoeur, Paul G. Schaberg, Geoffrey W. Wilson, Charles T. Driscoll, Timothy J. Fahey, Melany C. Fisk, Christine L. Goodale, Mark B. Green, Steven P. Hamburg, Chris E. Johnson, Mryon J. Mitchell, Jennifer L. Morse, Linda H. Pardo, Nicholas L. Rodenhouse Dec 2012

Long-Term Integrated Studies Show Complex And Surprising Effects Of Climate Change In The Northern Hardwood Forest, Peter M. Groffman, Lindsay E. Rustad, Pamela H. Templer, John L. Campbell, Lynn M. Christenson, Nina K. Lany, Anne M. Socci, Matthew A. Vadeboncoeur, Paul G. Schaberg, Geoffrey W. Wilson, Charles T. Driscoll, Timothy J. Fahey, Melany C. Fisk, Christine L. Goodale, Mark B. Green, Steven P. Hamburg, Chris E. Johnson, Mryon J. Mitchell, Jennifer L. Morse, Linda H. Pardo, Nicholas L. Rodenhouse

Environmental Science and Management Faculty Publications and Presentations

Evaluations of the local effects of global change are often confounded by the interactions of natural and anthropogenic factors that overshadow the effects of climate changes on ecosystems. Long-term watershed and natural elevation gradient studies at the Hubbard Brook Experimental Forest and in the surrounding region show surprising results demonstrating the effects of climate change on hydrologic variables (e.g., evapotranspiration, streamflow, soil moisture); the importance of changes in phenology on water, carbon, and nitrogen fluxes during critical seasonal transition periods; winter climate change effects on plant and animal community composition and ecosystem services; and the effects of anthropogenic disturbances and …


Site Selection By Migratory Shorebirds In Oregon Estuaries Over Broad And Fine Spatial Scales, Aileen Kilpatrick Miller Nov 2012

Site Selection By Migratory Shorebirds In Oregon Estuaries Over Broad And Fine Spatial Scales, Aileen Kilpatrick Miller

Dissertations and Theses

Many migratory shorebirds rely on estuaries as stop-over sites to refuel during migration, and the loss of stop-over sites is a primary threat to shorebird populations on the West Coast of the United States (e.g. Calidris alpina pacifica, C. mauri). Conservation and research has focused on the largest of these sites; however, smaller estuaries also host thousands of migratory shorebirds. Furthermore, the reasons for site selection are largely unknown. Estuarine inter-tidal microhabitats are non-uniform and both abiotic and biotic factors may serve as predictors of whether an abundance of shorebirds will use a site. I investigated shorebird site selection on …


Divergent Carbon Dynamics Under Climate Change In Forests With Diverse Soils, Tree Species, And Land Use Histories, Robert M. Scheller, Alec M. Kretchun, Steve Van Tuyl, Kenneth L. Clark, Melissa S. Lucash, John Hom Nov 2012

Divergent Carbon Dynamics Under Climate Change In Forests With Diverse Soils, Tree Species, And Land Use Histories, Robert M. Scheller, Alec M. Kretchun, Steve Van Tuyl, Kenneth L. Clark, Melissa S. Lucash, John Hom

Environmental Science and Management Faculty Publications and Presentations

Accounting for both climate change and natural disturbances—which typically result in greenhouse gas emissions—is necessary to begin managing forest carbon sequestration. Gaining a complete understanding of forest carbon dynamics is, however, challenging in systems characterized by historic over-utilization, diverse soils and tree species, and frequent disturbance. In order to elucidate the cascading effects of potential climate change on such systems, we projected forest carbon dynamics, including soil carbon changes, and shifts in tree species composition as a consequence of wildfires and climate change in the New Jersey pine barrens (NJPB) over the next 100 years. To do so, we used …


The Chemical Origin Of Behavior Is Rooted In Abiogenesis, Brian C. Larson, R. Paul Jensen, Niles Lehman Nov 2012

The Chemical Origin Of Behavior Is Rooted In Abiogenesis, Brian C. Larson, R. Paul Jensen, Niles Lehman

Chemistry Faculty Publications and Presentations

We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior. This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation …


Differential Effects Of The Hydrophobic Surfactant Proteins On The Formation Of Inverse Bicontinuous Cubic Phases, Mariya Chavarha, Ryan W. Loney, Kamlesh Kumar, Shankar B. Rananavare, Stephen B. Hall Nov 2012

Differential Effects Of The Hydrophobic Surfactant Proteins On The Formation Of Inverse Bicontinuous Cubic Phases, Mariya Chavarha, Ryan W. Loney, Kamlesh Kumar, Shankar B. Rananavare, Stephen B. Hall

Chemistry Faculty Publications and Presentations

Prior studies have shown that the biological mixture of the two hydrophobic surfactant proteins, SP-B and SP-C, produces faster adsorption of the surfactant lipids to an air/water interface, and that they induce 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE) to form inverse bicontinuous cubic phases. SP-B has a much greater effect than SP-C on adsorption. If the two proteins induce formation of the bicontinuous structures and faster adsorption by similar mechanisms, then they should also have differential ability to form the cubic phases. To test this hypothesis, we measured small angle X-ray scattering on the individual proteins combined with POPE. SP-B replicated the doserelated …


Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale Oct 2012

Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale

Biology Faculty Publications and Presentations

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an …


Phylotranscriptomics To Bring The Understudied Into The Fold: Monophyletic Ostracoda, Fossil Placement, And Pancrustacean Phylogeny, Todd H. Oakley, Joanna M. Wolfe, Annie R. Lindgren, Alexander K. Zaharoff Sep 2012

Phylotranscriptomics To Bring The Understudied Into The Fold: Monophyletic Ostracoda, Fossil Placement, And Pancrustacean Phylogeny, Todd H. Oakley, Joanna M. Wolfe, Annie R. Lindgren, Alexander K. Zaharoff

Biology Faculty Publications and Presentations

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We …


Sub-Antarctic And High Antarctic Notothenioid Fishes: Ecology And Adaptational Biology Revealed By The Icefish 2004 Cruise Of Rvib Nathaniel B. Palmer, H. William Detrich Iii, Bradley A. Buckley, Daniel F. Doolittle, Christopher D. Jones, Susanne J. Lockhart Sep 2012

Sub-Antarctic And High Antarctic Notothenioid Fishes: Ecology And Adaptational Biology Revealed By The Icefish 2004 Cruise Of Rvib Nathaniel B. Palmer, H. William Detrich Iii, Bradley A. Buckley, Daniel F. Doolittle, Christopher D. Jones, Susanne J. Lockhart

Biology Faculty Publications and Presentations

The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ecology, adaptational biology, community structure, and population dynamics of Antarctic notothenioid fishes relative to the cool/temperate notothenioids of the sub-Antarctic. To place this work in a comprehensive ecological context, cruise participants surveyed the benthos and geology of the biogeographic provinces and island shelves on either side of the Antarctic Polar Front (or Antarctic Convergence). Genome-enabled comparison of the responses of cold-living and temperate notothenioids to heat …


Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman Aug 2012

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biology Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …


Growing A Sustainable Portland Metropolitan Foodshed, Sheila Martin, Kathryn Doherty-Chapman, Robert Wise, Steve Foust, Kirsten Greene, Ellie Fiore, Ellen Wyoming, Clark Seavert, Rebecca Sullivan, Beth Emshoff, Anita Yap, Elise Scolnik, Bob Short Aug 2012

Growing A Sustainable Portland Metropolitan Foodshed, Sheila Martin, Kathryn Doherty-Chapman, Robert Wise, Steve Foust, Kirsten Greene, Ellie Fiore, Ellen Wyoming, Clark Seavert, Rebecca Sullivan, Beth Emshoff, Anita Yap, Elise Scolnik, Bob Short

Institute of Portland Metropolitan Studies Publications

Project Description and Objectives: Western Sustainable Agriculture Research and Education (SARE) provided funding for this study to examine key agricultural trends, identify producer needs and define strategies to strengthen the local food production system. The goals of the study are to: Define the Portland Metropolitan Foodshed; identify related agricultural and economic trends and develop a needs assessment based on input from producers and other stakeholders; assemble a regional toolkit of strategies to support evolution of a sustainable Portland Metropolitan Foodshed; work with the City of Damascus, Oregon to test the toolkit on a local level; Develop a research and educational …


Antisense Transcription Is Pervasive But Rarely Conserved In Enteric Bacteria, Rahul Raghavan, D. B. Sloan, H. Ochman Aug 2012

Antisense Transcription Is Pervasive But Rarely Conserved In Enteric Bacteria, Rahul Raghavan, D. B. Sloan, H. Ochman

Biology Faculty Publications and Presentations

Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To …


In Vivo Quantification Reveals Extensive Natural Variation In Mitochondrial Form And Function In Caenorhabditis Briggsae, Kiley Ann Hicks, Dana K. Howe, Aubrey Leung, Dee R. Denver, Suzanne Estes Aug 2012

In Vivo Quantification Reveals Extensive Natural Variation In Mitochondrial Form And Function In Caenorhabditis Briggsae, Kiley Ann Hicks, Dana K. Howe, Aubrey Leung, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential …


The Breeding Biology Of The Northern Pygmy Owl: Do The Smallest Of The Small Have An Advantage?, John F. Deshler, Michael T. Murphy Aug 2012

The Breeding Biology Of The Northern Pygmy Owl: Do The Smallest Of The Small Have An Advantage?, John F. Deshler, Michael T. Murphy

Biology Faculty Publications and Presentations

We explored the breeding biology of the Northern Pygmy-Owl (Glaucidium gnoma) from 2007 to 2009 in a forested reserve in Portland, Oregon. Large body size is often assumed to give animals reproductive advantages, and we tested whether body size affected timing of breeding and examined variation in diet, breeding date, clutch size, and reproductive success to explore whether the presumed benefits of large body size are evident in this species. The average size of 13 clutches was 5.8, and nest success was high (92%); 22 successful nests fledged an average of 5.2 young. Dates of first laying varied …


A Multi-Gene Phylogeny Of Cephalopoda Supports Convergent Morphological Evolution In Association With Multiple Habitat Shifts In The Marine Environment, Annie R. Lindgren, Molly S. Pankey, Frederick G. Hochberg, Todd H. Oakley Jul 2012

A Multi-Gene Phylogeny Of Cephalopoda Supports Convergent Morphological Evolution In Association With Multiple Habitat Shifts In The Marine Environment, Annie R. Lindgren, Molly S. Pankey, Frederick G. Hochberg, Todd H. Oakley

Biology Faculty Publications and Presentations

The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses …


Selfish Little Circles: Transmission Bias And Evolution Of Large Deletion-Bearing Mitochondrial Dna In Caenorhabditis Briggsae Nematodes, Katie A. Clark, Dana K. Howe, Kristin Gafner, Danika Kusuma, Sita Ping, Suzanne Estes Jul 2012

Selfish Little Circles: Transmission Bias And Evolution Of Large Deletion-Bearing Mitochondrial Dna In Caenorhabditis Briggsae Nematodes, Katie A. Clark, Dana K. Howe, Kristin Gafner, Danika Kusuma, Sita Ping, Suzanne Estes

Biology Faculty Publications and Presentations

Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ …


A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman Jun 2012

A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.

Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar …


A Genetic Study Of Ssv1, The Prototypical Fusellovirus, Eric Iverson, Kenneth M. Stedman Jun 2012

A Genetic Study Of Ssv1, The Prototypical Fusellovirus, Eric Iverson, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses of thermophilic Archaea are unique in both their structures and genomic sequences. The most widespread and arguably best studied are the lemon-shaped fuselloviruses. The spindle-shaped virus morphology is unique to Archaea but widespread therein. The best studied fusellovirus is SSV1 from Beppu, Japan, which infects Sulfolobus solfataricus. Very little is known about the function of the genes in the SSV1 genome. Recently we have developed genetic tools to analyze these genes. In this study, we have deleted three SSV1 open reading frames (ORFs) ranging from completely conserved to poorly conserved: VP2, d244, and b129. Deletion of the universally conserved …


Host Plant Use By Competing Acacia-Ants: Mutualists Monopolize While Parasites Share Hosts, Stefanie Kautz, Daniel J. Ballhorn, Johannes Kroiss, Steffen U. Pauls, Corrie S. Moreau, Sascha Eilmus, Erhard Strohm, Martin Heil May 2012

Host Plant Use By Competing Acacia-Ants: Mutualists Monopolize While Parasites Share Hosts, Stefanie Kautz, Daniel J. Ballhorn, Johannes Kroiss, Steffen U. Pauls, Corrie S. Moreau, Sascha Eilmus, Erhard Strohm, Martin Heil

Biology Faculty Publications and Presentations

Protective ant-plant mutualisms that are exploited by non-defending parasitic ants represent prominent model systems for ecology and evolutionary biology. The mutualist Pseudomyrmex ferrugineus is an obligate plant-ant and fully depends on acacias for nesting space and food. The parasite Pseudomyrmex gracilis facultatively nests on acacias and uses host-derived food rewards but also external food sources. Integrative analyses of genetic microsatellite data, cuticular hydrocarbons and behavioral assays showed that an individual acacia might be inhabited by the workers of several P. gracilis queens, whereas one P. ferrugineus colony monopolizes one or more host trees. Despite these differences in social organization, neither …


A Fast Response Highly Selective Probe For The Detection Of Glutathione In Human Blood Plasma, Yixing Guo, Xiaofeng Yang, Lovemore Hakuna, Aabha Barve, Jorge O. Escobedo, Mark Lowry, Robert M. Strongin May 2012

A Fast Response Highly Selective Probe For The Detection Of Glutathione In Human Blood Plasma, Yixing Guo, Xiaofeng Yang, Lovemore Hakuna, Aabha Barve, Jorge O. Escobedo, Mark Lowry, Robert M. Strongin

Chemistry Faculty Publications and Presentations

A fluorescent probe for glutathione (GSH) detection was developed. Our study indicates a possible mechanism which couples a conjugate addition and micelle-catalyzed large membered ring formation/elimination sequence. This method enables excellent selectivity towards GSH over other biological thiols such as cysteine (Cys) and homocysteine (Hcy). The proposed method is precise with a relative standard deviation (R.S.D) lower than 6% (n = 3) and has been successfully applied to determine GSH in human plasma with recoveries between 99.2% and 102.3%.


An Individual-Based Process Model To Simulate Landscape-Scale Forest Ecosystem Dynamics, Rupert Seidi, Werner Rammer, Robert M. Scheller, Thomas A. Spies Apr 2012

An Individual-Based Process Model To Simulate Landscape-Scale Forest Ecosystem Dynamics, Rupert Seidi, Werner Rammer, Robert M. Scheller, Thomas A. Spies

Environmental Science and Management Faculty Publications and Presentations

Forest ecosystem dynamics emerges from nonlinear interactions between adaptive biotic agents (i.e., individual trees) and their relationship with a spatially and temporally heterogeneous abiotic environment. Understanding and predicting the dynamics resulting from these complex interactions is crucial for the sustainable stewardship of ecosystems, particularly in the context of rapidly changing environmental conditions. Here we present iLand (the individual-based forest landscape and disturbance model), a novel approach to simulating forest dynamics as an emergent property of environmental drivers, ecosystem processes and dynamic interactions across scales. Our specific objectives were (i) to describe the model, in particular its novel approach to simulate …


Spatio-Temporal Differentiation And Sociality In Spiders, Jessica Purcell, João Vasconcellos-Neto, Jeffrey Alan Fletcher, Marcelo O. Gonzaga, Leticia Avilés Apr 2012

Spatio-Temporal Differentiation And Sociality In Spiders, Jessica Purcell, João Vasconcellos-Neto, Jeffrey Alan Fletcher, Marcelo O. Gonzaga, Leticia Avilés

Systems Science Faculty Publications and Presentations

Species that differ in their social system, and thus in traits such as group size and dispersal timing, may differ in their use of resources along spatial, temporal, or dietary dimensions. The role of sociality in creating differences in habitat use is best explored by studying closely related species or socially polymorphic species that differ in their social system, but share a common environment. Here we investigate whether five sympatric Anelosimus spider species that range from nearly solitary to highly social differ in their use of space and in their phenology as a function of their social system. By studying …


Evidence Of Reduced Arbuscular Mycorrhizal Fungal Colonization In Multiple Lines Of Bt Maize, Tanya E. Cheeke, Todd N. Rosenstiel, Mitchell B. Cruzan Apr 2012

Evidence Of Reduced Arbuscular Mycorrhizal Fungal Colonization In Multiple Lines Of Bt Maize, Tanya E. Cheeke, Todd N. Rosenstiel, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Premise of the Study: Insect-resistant Bacillus thuringiensis (Bt) maize is widely cultivated, yet few studies have examined the interaction of symbiotic arbuscular mycorrhizal fungi (AMF) with different lines of Bt maize. As obligate symbionts, AMF may be sensitive to genetic changes within a plant host. Previous evaluations of the impact of Bt crops on AMF have been inconsistent, and because most studies were conducted under disparate experimental conditions, the results are difficult to compare. Methods: We evaluate AMF colonization in nine Bt maize lines, differing in number and type of engineered trait, and five corresponding near-isogenic parental (P) base hybrids …


Evolution Finds Shelter In Small Spaces, Niles Lehman Apr 2012

Evolution Finds Shelter In Small Spaces, Niles Lehman

Chemistry Faculty Publications and Presentations

When RNA is replicated in cell-free systems, a ubiquitous problem is the hijacking of the system by short parasitic RNA sequences. In this issue of Chemistry & Biology, Bansho et al. show that compartmentalization into water-in-oil droplets can ameliorate this problem, but only if the droplets are small. This result helps to both recapitulate abiogenesis and optimize synthetic biology.

Refers to: Bansho, Yohsuke, et al. "Importance of Parasite RNA Species Repression for Prolonged Translation-Coupled RNA Self-Replication." Chemistry & Biology 19.4 (2012): 478-487.


4 Inches Of Living Soil: Teaching Biodiversity In The Learning Gardens–A Photo-Essay, Dilafruz R. Williams Mar 2012

4 Inches Of Living Soil: Teaching Biodiversity In The Learning Gardens–A Photo-Essay, Dilafruz R. Williams

Educational Leadership and Policy Faculty Publications and Presentations

In Learning Gardens and Sustainability Education: Bringing Life to Schools and Schools to Life, Williams and Brown (2011) place living soil at the center of the discourse on sustainability education. One of the seven principles that guides their pedagogy of learning gardens is: valuing biocultural diversity. This photo-essay of elementary students in K-8 schools, explores how 4 inches of soil in the learning gardens can teach about life’s diversity. The author urges humble attentiveness to that which is below our feet seemingly hidden and unnoticed yet teeming with life.


Associations Between The Quality Of The Residential Built Environment And Pregnancy Outcomes Among Women In North Carolina, Marie Lynn Miranda, Lynne C. Messer, Gretchen L. Kroeger Mar 2012

Associations Between The Quality Of The Residential Built Environment And Pregnancy Outcomes Among Women In North Carolina, Marie Lynn Miranda, Lynne C. Messer, Gretchen L. Kroeger

Community Health Faculty Publications and Presentations

Background: The built environment, a key component of environmental health, may be an important contributor to health disparities, particularly for reproductive health outcomes.Objective: In this study we investigated the relationship between seven indices of residential built environment quality and adverse reproductive outcomes for the City of Durham, North Carolina (USA).

Methods: We surveyed approximately 17,000 residential tax parcels in central Durham, assessing > 50 individual variables on each. These data, collected using direct observation, were combined with tax assessor, public safety, and U.S. Census data to construct seven indices representing impor­tant domains of the residential built environment: housing damage, property disorder, …


Links From Mantle To Microbe At The Lau Integrated Study Site: Insights From A Back-Arc Spreading Center, Margaret K. Tivey, Erin Becker, Roxanne Beinart, Charles R. Fisher, Peter Girguis, Charles H. Langmuir, Peter J. Michael, Anna-Louise Reysenbach Mar 2012

Links From Mantle To Microbe At The Lau Integrated Study Site: Insights From A Back-Arc Spreading Center, Margaret K. Tivey, Erin Becker, Roxanne Beinart, Charles R. Fisher, Peter Girguis, Charles H. Langmuir, Peter J. Michael, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and …


Pseudoscorpion Mitochondria Show Rearranged Genes And Genome-Wide Reductions Of Rna Gene Sizes And Inferred Structures, Yet Typical Nucleotide Composition Bias, Sergey Ovchinnikov, Susan E. Masta Mar 2012

Pseudoscorpion Mitochondria Show Rearranged Genes And Genome-Wide Reductions Of Rna Gene Sizes And Inferred Structures, Yet Typical Nucleotide Composition Bias, Sergey Ovchinnikov, Susan E. Masta

Biology Faculty Publications and Presentations

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do …


Northwest Forest Plan The First 15 Years (1994-2008): Watershed Condition Status And Trend, Steven H. Lanigan, Sean N. Gordon, Peter Eldred, Mark Isley, Heidi Anderson Feb 2012

Northwest Forest Plan The First 15 Years (1994-2008): Watershed Condition Status And Trend, Steven H. Lanigan, Sean N. Gordon, Peter Eldred, Mark Isley, Heidi Anderson

Institute for Sustainable Solutions Publications and Presentations

We used two data sets to evaluate stream and watershed condition for sixth-field watersheds in each aquatic province within the Northwest Forest Plan (NWFP) area: stream data and upslope data. The stream evaluation was based on inchannel data (e.g., substrate, pieces of large wood, water temperature, pool frequency, and macroinvertebrates) we sampled from 2002 to 2009 (193 watersheds) as part of a repeating sample design. We just completed our first round of sampling, so only current condition was calculated for this data set. When condition scores for the inchannel data were grouped into categories, relatively few fell into the low …