Biology Commons^™

Paternal Mitochondrial Transmission In Intra-Species Caenorhabditis Briggsae Hybrids, Joseph A. Ross, Dana K. Howe, Anna Luella Coleman-Hulbert, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

To study mitochondrial-nuclear genetic interactions in the nematode Caenorhabditis briggsae, our three laboratories independently created 38 intra-species cytoplasmic-nuclear hybrid (cybrid) lines. Although the cross design combines maternal mitotypes with paternal nuclear genotypes, eight lines (21%) unexpectedly contained paternal mitotypes. All eight share in common ancestry of one of two genetically related strains. This unexpected parallel observation of paternal mitochondrial transmission, undesirable given our intent of creating cybrids, provides a serendipitous experimental model and framework to study the molecular and evolutionary basis of uniparental mitochondrial inheritance.

Mitochondrial Dna Sequence And Lack Of Response To Anoxia In The Annual Killifish Austrofundulus Limnaeus, Josiah T. Wagner, Florisela H. Chavez, Jason E. Podrabsky

Biology Faculty Publications and Presentations

The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, …

Rare, Threatened And Endangered Species Of Oregon (2016), James S. Kagan, Sue Vrilakas, John A. Christy, Eleanor P. Gaines, Lindsey Wise, Cameron Pahl, Kathy Howell

Institute for Natural Resources Publications

Extinction is a natural process. Today, however, plant and animal species are disappearing world-wide at an accelerated pace. Based on current trends, half of the species on earth will be extinct within the next 100 years. The major reasons for this are human caused changes to the environment, which continue to increase - in Oregon and throughout the world.

Once lost, a species can never be recovered, and there is no way of knowing how useful it may have been. We do know that human beings and many of their industries depend on plant and animal products. About 50% of …

The Intervening Sequence Of Coxiella Burnetii: Characterization And Evolution, Indu Warrier, Mathias C. Walter, Dimitrios Frangoulidis, Rahul Raghavan, Linda D. Hicks, Michael F. Minnick

Biology Faculty Publications and Presentations

The intervening sequence (IVS) of Coxiella burnetii, the agent of Q fever, is a 428-nt selfish genetic element located in helix 45 of the precursor 23S rRNA. The IVS element, in turn, contains an ORF that encodes a hypothetical ribosomal S23 protein (S23p). Although S23p can be synthesized in vitro in the presence of an engineered E. coli promoter and ribosome binding site, results suggest that the protein is not synthesized in vivo. In spite of a high degree of IVS conservation among different strains of C. burnetii, the region immediately upstream of the S23p start codon …

Coevolution Of Cyanogenic Bamboos And Bamboo Lemurs On Madagascar, Daniel J. Ballhorn, Fanny Patrika Rakotoarivelo, Stefanie Kautz

Biology Faculty Publications and Presentations

Feeding strategies of specialist herbivores often originate from the coevolutionary arms race of plant defenses and counter-adaptations of herbivores. The interaction between bamboo lemurs and cyanogenic bamboos on Madagascar represents a unique system to study diffuse coevolutionary processes between mammalian herbivores and plant defenses. Bamboo lemurs have different degrees of dietary specialization while bamboos show different levels of chemical defense. In this study, we found variation in cyanogenic potential (HCNp) and nutritive characteristics among five sympatric bamboo species in the Ranomafana area, southeastern Madagascar. The HCNp ranged from 209±72 μmol cyanide* g^-1 dwt in Cathariostachys madagascariensis to no cyanide …

Genomics-Informed Isolation And Characterization Of A Symbiotic Nanoarchaeota System From A Terrestrial Geothermal Environment, Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, Mircea Podar

Biology Faculty Publications and Presentations

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and …

Recumbence Behavior In Zoo Elephants: Determination Of Patterns And Frequency Of Recumbent Rest And Associated Environmental And Social Factors, Matthew Robert Holdgate, Cheryl L. Meehan, Jennifer N. Hogan, Lance J. Miller, Jeff Rushen, Anne-Marie De Passillé, Josesph Soltis, Jeff Andrews, David J. Shepherdson

Biology Faculty Publications and Presentations

Resting behaviors are an essential component of animal welfare but have received little attention in zoological research. African savanna elephant (Loxodonta africana) and Asian elephant (Elephas maximus) rest includes recumbent postures, but no large-scale investigation of African and Asian zoo elephant recumbence has been previously conducted. We used anklets equipped with accelerometers to measure recumbence in 72 adult female African (n = 44) and Asian (n = 28)elephants housed in 40 North American zoos. We collected 344 days of data and determined associations between recumbence and social, housing, management, and demographic factors. African elephants were recumbent less (2.1 hours/day, S.D. …

Bayesian Methods For Comparing Species Physiological And Ecological Response Curves, Michael B. Ashcroft, Angélica Casanova-Katny, Kerrie Mengersen, Todd N. Rosenstiel, Johanna D. Turnbull, Jane Wasley, Melinda J. Waterman, Gustavo E. Zúñiga, Sharon A. Robinson

Biology Faculty Publications and Presentations

Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species' responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. …

Walking Behavior Of Zoo Elephants: Associations Between Gps-Measured Daily Walking Distances And Environmental Factors, Social Factors, And Welfare Indicators, Matthew Robert Holdgate, Cheryl L. Meehan, Jennifer N. Hogan, Lance J. Miller, Josesph Soltis, Jeff Andrews, David J. Shepherdson

Biology Faculty Publications and Presentations

Research with humans and other animals suggests that walking benefits physical health. Perhaps because these links have been demonstrated in other species, it has been suggested that walking is important to elephant welfare, and that zoo elephant exhibits should be designed to allow for more walking. Our study is the first to address this suggestion empirically by measuring the mean daily walking distance of elephants in North American zoos, determining the factors that are associated with variations in walking distance, and testing for associations between walking and welfare indicators. We used anklets equipped with GPS data loggers to measure outdoor …

The Other Lives Of Ribosomal Proteins, Metrah M. Nader

PSU McNair Scholars Online Journal

Cellular mRNAs are produced in the nucleus and exported to the cytoplasm through nuclear pore complexes (NPC) that are found in the nuclear membrane. The correctly processed mRNAs are exported in the form of messenger ribonucleoproteins (mRNPs). Since the NPC allows the passage of only one mRNA molecule at a time, export of large ribonucleoproteins (megaRNP) found in the nucleus cannot be transported through the NPC. However, a recent study has discovered an alternative export mechanism known as nuclear envelope budding, which allows megaRNP granules to be exported. This study particularly focuses on identifying ribosomal proteins (RPs) found within large …

Gene Expression Patterns Of Bone Morphogenetic Proteins (Bmps) During Early Embryonic Development In The Annual Killifish Austrofundulus Limnaeus, Eva Y. Chan

PSU McNair Scholars Online Journal

The developmental pattern of the annual killifish Austrofundulus limnaeus is unusual compared to other fish. First, the cell movements associated with gastrulation are separated from formation of the embryonic axis. In addition, embryonic diapause can occur. Diapause II and III are often observed when embryos are incubated at 25^oC. Maternal influences and incubation environment are the factors that determine entrance into embryonic diapause, but the molecular mechanisms that regulate diapause are still unknown. Interestingly, embryonic diapause and the unusual cell movements observed during early development are always found together in species of annual killifish that exhibit diapause. Bone …

Investigating The Origin And Functions Of A Novel Small Rna In Escherichia Coli, Fenil Rashmin Kacharia

Dissertations and Theses

Non-coding small RNAs (sRNAs) regulate various cellular processes in bacteria. They bind to a chaperone protein Hfq for stability and regulate gene expression by base-pairing with target mRNAs. Although the importance of sRNAs in bacteria has been well established, the mode of origination of novel sRNA genes is still elusive, mainly because the rapid rate of evolution of sRNAs obscures their original sources. To overcome this impediment, we identified a recently formed sRNA (EcsR2) in E. coli, and show that it evolved from a degraded bacteriophage gene. Our analyses also revealed that young sRNAs such as EcsR2 are expressed …

Stranding Mortality Patterns In California Sea Lions And Steller Sea Lions In Oregon And Southern Washington, 2006 To 2014, Kessina Lee

Dissertations and Theses

As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts with commercial and recreational fisheries. An analysis of strandings of California sea lions, Zalophus californianus, and Steller sea lions, Eumetopias jubatus, from 2006 to 2014, included cause of death, changing ocean conditions, and anthropogenic activity. Causes of death included disease, injury, and human interaction, such as gunshot wounds, fisheries net entanglements and boat strikes.

Oregon and Washington strandings of California sea lions are primarily adult and …

Investigating The Effects Of 17Α-Ethynylestradiol On Mitochondrial Genome Stability, Alicia M. Chivers

Dissertations and Theses

Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA …

Friend Or Foe—Light Availability Determines The Relationship Between Mycorrhizal Fungi, Rhizobia And Lima Bean (Phaseolus Lunatus L.), Daniel J. Ballhorn, Martin Schädler, Jacob D. Elias, Jess A. Millar, Stefanie Kautz

Biology Faculty Publications and Presentations

Plant associations with root microbes represent some of the most important symbioses on earth. While often critically promoting plant fitness, nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) also demand significant carbohydrate allocation in exchange for key nutrients. Though plants may often compensate for carbon loss, constraints may arise under light limitation when plants cannot extensively increase photosynthesis. Under such conditions, costs for maintaining symbioses may outweigh benefits, turning mutualist microbes into parasites, resulting in reduced plant growth and reproduction. In natural systems plants commonly grow with different symbionts simultaneously which again may interact with each other. This might add complexity …

The Value Of Long-Term Stream Invertebrate Data Collected By Citizen Scientists, Patrick M. Edwards

Environmental Science and Management Faculty Publications and Presentations

The purpose of this investigation was to systematically examine the variability associated with temporally-oriented invertebrate data collected by citizen scientists and consider the value of such data for use in stream management. Variability in invertebrate data was estimated for three sources of variation: sampling, within-reach spatial and long-term temporal. Long-term temporal data were also evaluated using ordinations and an Index of Biotic Integrity (IBI). Through two separate investigations over an 11-year study period, participants collected more than 400 within-reach samples during 44 sampling events at three streams in the western United States. Within-reach invertebrate abundance coefficient of variation (CV) ranged …

Seasonal And Sex Differences In Responsiveness To Adrenocorticotropic Hormone Contribute To Stress Response Plasticity In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis), Catherine A. Dayger, Deborah I. Lutterschmidt

Biology Faculty Publications and Presentations

Like many vertebrates, hormonal responses to stress vary seasonally in red-sided garter snakes (Thamnophis sirtalis parietalis). For example, males generally exhibit reduced glucocorticoid responses to a standard stressor during the spring mating season. We asked whether variation in adrenal sensitivity to adrenocorticotropic hormone (ACTH) explains why glucocorticoid responses to capture stress vary with sex, season, and body condition in red-sided garter snakes. We measured glucocorticoids at 0, 1, and 4 hours after injection with ACTH (0.1 IU/g body mass) or vehicle in males and females during the spring mating season and fall pre-hibernation period. Because elevated glucocorticoids can influence sex …

Paths Of Heritable Mitochondrial Dna Mutation And Heteroplasmy In Reference And Gas-1 Strains Of Caenorhabditis Elegans, Riana I. Wernick, Suzanne Estes, Dana K. Howe, Dee R. Denver

Biology Faculty Publications and Presentations

Heteroplasmy—the presence of more than one mitochondrial DNA (mtDNA) sequence type in a cell, tissue, or individual—impacts human mitochondrial disease and numerous aging-related syndromes. Understanding the trans-generational dynamics of mtDNA is critical to understanding the underlying mechanisms of mitochondrial disease and evolution. We investigated mtDNA mutation and heteroplasmy using a set of wild-type (N2 strain) and mitochondrial electron transport chain (ETC) mutant (gas-1) mutant Caenorhabditis elegans mutation-accumulation (MA) lines. The N2 MA lines, derived from a previous experiment, were bottlenecked for 250 generations. The gas-1 MA lines were created for this study, and bottlenecked in the laboratory for …

Mechanisms Of Methane Transport Through Populus Trichocarpa, Ellynne Marie Kutschera, M. A. K. Khalil, Andrew Rice, Todd Rosenstiel

Physics Faculty Publications and Presentations

Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global CH4 emission and the mechanisms of tree transport are relatively unknown. CH4 emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to CH4 enriched water and canopy emissions of CH4 were measured. The average flux for 34 trials (at temperatures ranging from 17 to 25 °C) was 2.8 ± 2.2 …

Is Protection Against Florivory Consistent With The Optimal Defense Hypothesis?, Adrienne L. Godschalx, Lauren Stady, Benjamin Watzig, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Background: Plant defense traits require resources and energy that plants may otherwise use for growth and reproduction. In order to most efficiently protect plant tissues from herbivory, one widely accepted assumption of the optimal defense hypothesis states that plants protect tissues most relevant to fitness. Reproductive organs directly determining plant fitness, including flowers and immature fruit, as well as young, productive leaf tissue thus should be particularly well-defended. To test this hypothesis, we quantified the cyanogenic potential (HCNp)—a direct, chemical defense—systemically expressed in vegetative and reproductive organs in lima bean (Phaseolus lunatus), and we tested susceptibility of these …

Sex-Specific Fungal Communities Of The Dioicous Moss Ceratodon Purpureus, Mehmet Ali Balkan

Dissertations and Theses

Mosses display a number of hallmark life history traits that influence their ecology at the population and community level. The long lived separation of sexes observed in the haploid gametophyte (dioicy) is one such feature of particular importance, as it is observed in the majority of bryophytes and creates intraspecific specialization of male and female individuals.

The prevalence of sexually dimorphic mosses raises the possibility of sex-specific interactions with fungi as observed in some vascular plants. Here I investigated how moss sex shapes fungal communities associated with gametophytic tissues of the ubiquitous moss, Ceratodon purpureus. Using greenhouse populations of …

Three Simple Experiments To Examine The Effect Of Sediment Pollution On Algae-Based Food Webs In Streams, Patrick M. Edwards, Rodney Shroufe

Environmental Science and Management Faculty Publications and Presentations

Streams and stream macroinvertebrates are ideal natural systems for ecological inquiry. We present three simple experiments that students can use to conduct field-based investigations which illustrate the importance of algae-based food webs in streams and measure the effects of sediment pollution (scour and deposition) on stream ecological processes. Over the past 5 years, we have conducted these experiments 19 times with our students. We report on the results and reliability of these experiments and make suggestions for other educators who may want to conduct them.

Small Unmanned Aerial Vehicles (Micro-Uavs, Drones) In Plant Ecology, Mitchell B. Cruzan, Ben G. Weinstein, Monica R. Grasty, Brendan F. Kohrn, Elizabeth C. Hendrickson, Tina M. Arredondo, Pamela G. Thompson

Biology Faculty Publications and Presentations

Premise of the study: Low-elevation surveys with small aerial drones (micro–unmanned aerial vehicles [UAVs]) may be used for a wide variety of applications in plant ecology, including mapping vegetation over small- to medium-sized regions. We provide an overview of methods and procedures for conducting surveys and illustrate some of these applications.

Methods: Aerial images were obtained by flying a small drone along transects over the area of interest. Images were used to create a composite image (orthomosaic) and a digital surface model (DSM). Vegetation classification was conducted manually and using an automated routine. Coverage of an individual species …

Free Mate Choice Enhances Conservation Breeding In The Endangered Giant Panda, Meghan S. Martin-Wintle, David J. Shepherdson, Guiquan Zhang, Hemin Zhang, Desheng Li, Xiaoping Zhou, Rengui Li, Ronald R. Swaisgood

Biology Faculty Publications and Presentations

Conservation breeding programmes have become an increasingly important tool to save endangered species, yet despite the allocation of significant resources, efforts to create self-sustaining populations have met with limited success. The iconic giant panda (Ailuropoda melanoleuca) embodies the struggles associated with ex situ species conservation. Here we show that behavioural mate preferences in giant pandas predict reproductive outcomes. Giant pandas paired with preferred partners have significantly higher copulation and birth rates. Reproductive rates increase further when both partners show mutual preference for one another. If managers were to incorporate mate preferences more fully into breeding management, the production of giant …

Moss In The Classroom: A Tiny But Mighty Tool For Teaching Biology, Erin E. Shortlidge, James R. Hashimoto

Biology Faculty Publications and Presentations

Here we present a mechanism to infuse ecology into the classroom using a broadly adaptable system. We developed a novel moss-based project that introduces research-based experiences for middle school students, and can be modified for integration into K-16 classrooms. The project is ecologically relevant, facilliating opportunities for students to experience intimate interactions with ecosystem subtleties by asking their own questions. We describe and suggest how students can develop, build, test, and assess microcosm experiments of their own design, learning the process of science by “doing science.” Details on project execution, representative examples of distinctive research-question-based projects are presented. We aim …

Genome Rearrangements Can Make And Break Small Rna Genes, Rahul Raghavan, Fenil R. Kacharia, Jess A. Millar, Christine Demko Sislak, Howard Ochman

Biology Faculty Publications and Presentations

Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in …

The Impeccable Timing Of The Apple Maggot Fly, Rhagoletis Pomonella (Dipetera: Tephritidae), And Its Implications For Ecological Speciation, Monte Arthur Mattsson

Dissertations and Theses

Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping explain the role of ecology in generating biodiversity. Adaptive radiations are often propelled by selective fitness tradeoffs experienced by individuals that invade new habitats, resulting in reproductive isolation from ancestral conspecifics and potentially cladogenesis. Host specialist insects are among the most speciose organisms known and serve as highly useful models for studying adaptive radiations. We are just beginning to understand the pace and degree with which these insects diversify. The apple maggot, Rhagoletis …

Degradation By Cullin 3 And Effect On Wnk Kinases Suggest A Role Of Klhl2 In The Pathogenesis Of Familial Hyperkalemic Hypertension, Chong Zhang, Nicholas P. Meermeier, Andrew Terker, Katharina I. Blankenstein, Jeffrey D. Singer, Juliette Hadchouel, David Ellison, Chao-Ling Yang

Biology Faculty Publications and Presentations

Mutations in WNK1 and WNK4, and in components of the Cullin-Ring Ligase system, kelch-like 3 (KLHL3) and Cullin 3 (CUL3), can cause the rare hereditary disease, Familial Hyperkalemic Hypertension (FHHt). The disease is characterized by overactivity of the renal sodium chloride cotransporter (NCC), which is phosphorylated and activated by the WNK-stimulated Ste20-type kinases, SPAK and OSR1. WNK kinases themselves can be targeted for ubiquitination and degradataion by the CUL3-KLHL3 E3 ubiquitin ligase complex. It is unclear, however, why there are significant differences in phenotypic severity among FHHt patients with mutations in different genes. It was reported that kelch-like 2 (KLHL2), …

Saccular Transcriptome Profiles Of The Seasonal Breeding Plainfin Midshipman Fish (Porichthys Notatus), A Teleost With Divergent Sexual Phenotypes, Joshua J. Faber-Hammond, Manoj P. Samanta, Elizabeth A. Whitchurch, Dustin Manning, Joseph A. Sisneros, Allison B. Coffin

Biology Faculty Publications and Presentations

Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus). During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker) males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ) as one possible target for this seasonal modulation. Here …

Rapid And Repeatable Shifts In Life-History Timing Of Rhagoletis Pomonella (Diptera: Tephritidae) Following Colonization Of Novel Host Plants In The Pacific Northwestern United States, Monte Mattsson, Glen R. Hood, Jeffery L. Feder, Luis A. Ruedas

Biology Faculty Publications and Presentations

Host shifts of phytophagous insect specialists to novel plants can result in divergent ecological adaptation, generating reproductive isolation and potentially new species. Rhagoletis pomonellafruit flies in eastern North America underwent a host shift ~160 ya from native downy hawthorn (Crataegus mollis) to introduced, domesticated apple (Malus domestica). Divergent selection on diapause phenology related to the earlier fruiting time of apples versus downy hawthorns resulted in partial allochronic reproductive isolation between the fly races. Here, we test for how rapid and repeatable shifts in life-history timing are driving ecological divergence of R. pomonella in the Pacific …