Biology Commons^™

Snowy Plover Buried Alive By Wind-Blown Sand, J. Daniel Farrar, Adam A. Kotaich, David J. Lauten, Kathleen A. Castelein, Eleanor P. Gaines

Institute for Natural Resources Publications

Brief description of an encounter with a Snowy Plover discovered at a nest site near the mouth of Tahkenitch Creek in Douglas County, Oregon. The plover was buried up to its neck in sand, presumably caused by high winds. The article describes the authors' efforts to resuscitate the plover.

In Vivo Quantification Of Reactive Oxygen Species Demonstrates High Levels Of Oxidative Stress In Base Excision Repair-Deficient Caenorhabditis Elegans: Implications For Associative Metabolic Phenotypes, Travis Lee Hase

University Honors Theses

In this present study, I use C. elegans as a model organism to better characterize the phenotypic response to deficiencies in base excision repair (BER). This will help to elucidate how DNA damage, increased mutagenesis, and exposure to reactive oxygen species (ROS) is related to Metabolic Syndrome. Additionally, this work will establish a starting point for investigation that can further characterize phenotypic responses such as mitochondrial physiology and morphology through measurements of mitochondrial membrane potential and mitochondrial circularity. The overall goal of this research is to better understand the nature of mitochondrial dysfunction with respect to the inactivation of DNA …

Inefficient Replication Reduces Reca-Mediated Repair Of Uvdamaged Plasmids Introduced Into Competent Escherichia Coli, Harout Arthur Jeiranian, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

Transformation of Escherichia coli with purified plasmids containing DNA damage is frequently used as a tool to characterize repair pathways that operate on chromosomes. In this study, we used an assay that allowed us to quantify plasmid survival and to compare how efficiently various repair pathways operate on plasmid DNA introduced into cells relative to their efficiency on chromosomal DNA. We observed distinct differences between the mechanisms operating on the transforming plasmid DNA and the chromosome. An average of one UV-induced lesion was sufficient to inactivate ColE1-based plasmids introduced into nucleotide excision repair mutants, suggesting an essential role for repair …

Uvrd Participation In Nucleotide Excision Repair Is Required For The Recovery Of Dna Synthesis Following Uv-Induced Damage In Escherichia Coli, Kelley Nicole Newton, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

UvrD is a DNA helicase that participates in nucleotide excision repair and several replication-associated processes, including methyl-directed mismatch repair and recombination. UvrD is capable of displacing oligonucleotides from synthetic forked DNA structures in vitro and is essential for viability in the absence of Rep, a helicase associated with processing replication forks. These observations have led others to propose that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forks in vivo has not been directly examined. In this study, we characterized the role UvrD has in processing …

A Selective Force Favoring Increased G+C Content In Bacterial Genes, Rahul Raghavan, Yogeshwar D. Kelkar, Howard Ochman

Biology Faculty Publications and Presentations

Bacteria display considerable variation in their overall base compositions, which range from 13% to over 75% G+C. This variation in genomic base compositions has long been considered to be a strictly neutral character, due solely to differences in the mutational process; however, recent sequence comparisons indicate that mutational input alone cannot produce the observed base compositions, implying a role for natural selection. Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help shape the overall genomic base composition. To explore this possibility, we tested whether genes that encode the same protein …

Genomic Amplification Of An Endogenous Retrovirus In Zebrafish T-Cell Malignancies, J. Kimble Frazer, Lance A. Batchelor, Diana F. Bradley, Kim H. Brown, Kimberly P. Dobrinski, Charles Lee, Nikolaus S. Trede

Biology Faculty Publications and Presentations

Genomic instability plays a crucial role in oncogenesis. Somatically acquiredmutations can disable some genes and inappropriately activate others. In addition, chromosomal rearrangements can amplify, delete, or even fuse genes, altering their functions and contributing to malignant phenotypes. Using array comparative genomic hybridization (aCGH), a technique to detect numeric variations between different DNA samples, we examined genomes from zebrafish (Danio rerio) T-cell leukemias of three cancerprone lines. In all malignancies tested, we identified recurring amplifications of a zebrafish endogenous retrovirus. This retrovirus, ZFERV, was first identified due to high expression of proviral transcripts in thymic tissue from larval and adult fish.We …

Anoxia Tolerance During Vertebrate Development - Insights From Studies On The Annual Killifish Austrofundulus Limnaeus, Jason E. Podrabsky, Claire L. Riggs, Jeffrey M. Duerr

Biology Faculty Publications and Presentations

This is chapter 1 from Anoxia -- This book reviews how severe oxygen deprivation affects biological systems - from the molecular to the ecological level. The contributing authors come from diverse regions of the world, which proves the interest in the academic analysis of oxygen deprivation. The diversity in the experimental approach scientists take, in order to understand the influence oxygen deprivation has on living systems, is apparent throughout this book. One of the presented ideas deals with the exploration and examination of the physiological, cellular and genetic characteristics of killifish embryos and nematodes exposed to anoxia. Furthermore, the book …

The Role Of Nucleotide Excision Repair In Restoring Replication Following Uv-Induced Damage In Escherichia Coli, Kelley Nicole Newton

Dissertations and Theses

Following low levels of UV exposure, Escherichia coli cells deficient in nucleotide excision repair recover and synthesize DNA at near wild type levels, an observation that formed the basis of the post replication recombination repair model. In this study, we characterized the DNA synthesis that occurs following UV-irradiation in the absence of nucleotide excision repair and show that although this synthesis resumes at near wild type levels, it is coincident with a high degree of cell death. We confirm that the replication occurring under these conditions involves extensive levels of strand exchange. However, cells undergoing this form of replication accumulate …

Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, Kiley Ann Hicks

Dissertations and Theses

Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis …

Ultrasonic Wave Propagation Assessment Of Native Cartilage Explants And Hydrogel Scaffolds For Tissue Engineering, Sean S. Kohles, Shelley S. Mason, Anya P. Adams, Robert J. Berg, Jessica Blank, Fay Gibson, Johnathan Righetti, Lesha S. Washington, Asit K. Saha

Mechanical and Materials Engineering Faculty Publications and Presentations

Non-destructive techniques characterising the mechanical properties of cells, tissues, and biomaterials provide baseline metrics for tissue engineering design. Ultrasonic wave propagation and attenuation has previously demonstrated the dynamics of extracellular matrix synthesis in chondrocyte-seeded hydrogel constructs. In this paper, we describe an ultrasonic method to analyse two of the construct elements used to engineer articular cartilage in real-time, native cartilage explants and an agarose biomaterial. Results indicated a similarity in wave propagation velocity ranges for both longitudinal (1500-1745 m/s) and transverse (350-950 m/s) waveforms. Future work will apply an acoustoelastic analysis to distinguish between the fluid and solid properties including …

Limits To Sexual Reproduction In Geothermal Bryophytes, Sarah M. Eppley, Todd N. Rosenstiel, Camille Brianne Graves, Estefanía Llaneza García

Biology Faculty Publications and Presentations

Previous research suggests that while sexual reproduction generally increases with environmental stress it may decrease with extreme stress, at the edge of eukaryotic life. In this study, we explored the limits to sexual reproduction in an extremophile, bryophyte system to ultimately understand the processes that limit sexual reproduction. We used field data from geothermal sites at Lassen Volcanic National Park, California, to demonstrate that sexual reproduction, as measured by the number of sporophytes per shoot, decreases with increasing environmental stress. We found that the number of sporophytes per shoot is positively correlated with distance from geothermal features. When Pohlia nutans …

Multistate Mark-Recapture Analysis Reveals No Effect Of Blood Sampling On Survival And Recapture Of Eastern Kingbirds (Tyrannus Tyrannus), Lucas J. Redmond, Michael T. Murphy

Biology Faculty Publications and Presentations

The experimentally supported and prevailing opinion is that blood sampling has few to no long-term effects on survival of birds when conducted properly, and blood sampling has become a vital addition to the toolbox of many ornithologists. However, many of the studies that concluded that blood sampling had negligible effects on birds used approaches that did not account for temporary emigration and probability of capture. To date, the only study to have done so found that blood sampling had a strong negative effect on survival. We conducted a mark–recapture analysis of 8 years of banding and bleeding data on Eastern …

Growth Phase-Dependent Gene Regulation In Vivo In Sulfolobus Solfataricus, Melissa Deyoung, Michelle Thayer, John Van Der Oost, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Ribosomal genes are strongly regulated dependent on growth phase in all organisms, but this regulation is poorly understood in Archaea. Moreover, very little is known about growth phase-dependent gene regulation in Archaea. SSV1- based lacS reporter gene constructs containing the Sulfolobus 16S/23S rRNA gene core promoter, the TF55a core promoter, or the native lacS promoter were tested in Sulfolobus solfataricus cells lacking the lacS gene. The 42-bp 16S/23S rRNA gene and 39-bp TF55a core promoters are sufficient for gene expression in S. solfataricus. However, only gene expression driven by the 16S/23S rRNA gene core promoter is dependent on …

Escherichia Coli Fpg Glycosylase Is Nonrendundant And Required For The Rapid Global Repair Of Oxidized Purine And Pyrimidine Damage In Vivo, Brandy J. Schalow, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

Endonuclease (Endo) III and formamidopyrimidine-N-glycosylase (Fpg) are two of the predominant DNA glycosylases in Escherichia coli that remove oxidative base damage. In cell extracts and purified form, Endo III is generally more active toward oxidized pyrimidines, while Fpg is more active towards oxidized purines. However, the substrate specificities of these enzymes partially overlap in vitro. Less is known about the relative contribution of these enzymes in restoring the genomic template following oxidative damage. In this study, we examined how efficiently Endo III and Fpg repair their oxidative substrates in vivo following treatment with hydrogen peroxide. We found …

Natural Variation In Life History And Aging Phenotypes Is Associated With Mitochondrial Dna Deletion Frequency In Caenorhabditis Briggsae, Suzanne Estes, Anna Luella Coleman-Hulbert, Kiley Ann Hicks, Gene De Haan, Sarah R. Martha, Jeremiah B. Knapp, Samson William Smith, Kevin C. Stein, Dee R. Denver

Biology Faculty Publications and Presentations

Background: Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial dysfunction in aging processes has been the lack of model systems with relevant, naturally occurring mitochondrial genetic variation. Toward the goal of developing such a model system, we studied natural variation in life history, metabolic, and aging phenotypes as it relates to levels of a naturally-occurring heteroplasmic mitochondrial ND5 deletion recently discovered to segregate among wild populations of the soil nematode, Caenorhabditis briggsae. The normal product of ND5 is a central component of the …

Genome-Wide Detection Of Novel Regulatory Rnas In E. Coli, Rahul Raghavan, Eduardo Groisman, Howard Ochman

Biology Faculty Publications and Presentations

The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein …

Molecular Genetic Analysis Of Creld1 In Patients With Heterotaxy Disorder, Samaneh Zhian

Dissertations and Theses

Heterotaxy refers to the abnormal arrangement of internal organs in relation to each other. Model organism studies have shown that functions of more than eighty genes are required for normal asymmetric left-right organ development. CRELD1 has been shown to be necessary for proper heart development and mutations in CRELD1 are known to increase risk of cardiac atrioventricular septal defects (AVSD). AVSD is the most common form of heart defect associated with heterotaxy, and we have previously shown that some individuals heterotaxy-related AVSD have mutations in CRELD1.

Therefore, we propose to examine the CRELD1 gene in a large sample of …

Population Structure Of Island-Associated Pantropical Spotted Dolphins (Stenella Attenuata) In Hawaiian Waters, Sarah Shelby Courbis

Dissertations and Theses

Understanding gene flow, diversity, and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on dolphin populations. With the very recent exceptions of false killer whales (Pseudorca crassidens), spinner dolphins (Stenella longirostris), and common bottlenose dolphins (Tursiops truncatus), Hawaiian odontocete species are managed as single stocks within the U.S. Hawaiian Exclusive Economic Zone. These exceptions are a result of recent studies that have indicated that some species have populations that show fidelity to individual islands or groups of islands, resulting in genetic differentiation, often with management implications. The first part …

Complexity Through Recombination: From Chemistry To Biology, Niles Lehman, Carolina Diaz Arenas, Wesley A. White, Francis J. Schmidt

Chemistry Faculty Publications and Presentations

Recombination is a common event in nature, with examples in physics, chemistry, and biology. This process is characterized by the spontaneous reorganization of structural units to form new entities. Upon reorganization, the complexity of the overall system can change. In particular the components of the system can now experience a new response to externally applied selection criteria, such that the evolutionary trajectory of the system is altered. In this work we explore the link between chemical and biological forms of recombination. We estimate how the net system complexity changes, through analysis of RNA-RNA recombination and by mathematical modeling. Our results …

Rare, Threatened And Endangered Species Of Oregon (2010), James S. Kagan, Sue Vrilakas, Eleanor P. Gaines, Cliff Alton, Lindsey Koepke, John A. Christy, Erin Doyle

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 cause of this phenomenon is 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% …

Biological Computation, Melanie Mitchell

Computer Science Faculty Publications and Presentations

In this article, the term biological computation refers to the proposal that living organisms themselves perform computations, and, more specifically, that the abstract ideas of information and computation may be key to understanding biology in a more unified manner. It is important to point out that the study of biological computation is typically not the focus of the field of computational biology, which applies computing tools to the solution of specific biological problems. Likewise, biological computation is distinct from the field of biologically-inspired computing, which borrows ideas from biological systems such as the brain, insect colonies, and the immune system …

Pcif1 Modulates Pdx1 Protein Stability And Pancreatic Β Cell Function And Survival In Mice, Kathryn C. Claiborn, Mira M. Sachdeva, Corey E. Cannon, David N. Groff, Jeffrey D. Singer, Doris A. Stoffers

Biology Faculty Publications and Presentations

The homeodomain transcription factor pancreatic duodenal homeobox 1 (Pdx1) is a major mediator of insulin transcription and a key regulator of the β cell phenotype. Heterozygous mutations in PDX1 are associated with the development of diabetes in humans. Understanding how Pdx1 expression levels are controlled is therefore of intense interest in the study and treatment of diabetes. Pdx1 C terminus–interacting factor-1 (Pcif1, also known as SPOP) is a nuclear protein that inhibits Pdx1 transactivation. Here, we show that Pcif1 targets Pdx1 for ubiquitination and proteasomal degradation. Silencing of Pcif1 increased Pdx1 protein levels in cultured mouse β cells, and Pcif1 …

Biogeography Of The American Pika (Ochotona Princeps) In Oregon And Southern Washington: Illuminating Genetic Relationships Among Disjunct Populations, George Washington Batten Iii

Dissertations and Theses

The American pika (Ochotona princeps) finds moderately warm temperatures (>25°C) lethally stressful, and at the end of the last Ice Age 10,000 years ago was forced to disperse to cooler, "sky island" mountaintops where they are almost exclusively found today. Thirty six subspecies are recognized, all established using morphological characters, and it is uncertain whether these subspecies' designations are corroborated by genetic analyses. This study elucidates three hypotheses regarding populations in Oregon and southern Washington: 1) O. p. fumosa constitutes a subspecies distinct form O. p. brunnescens, 2) the Columbia River constitutes a barrier to gene …

Selection Ratios On Community Aggregated Traits To Estimate Ecological Filters Imposed On Species By Sites, Nathanael I. Lichti, Michael T. Murphy

Biology Faculty Publications and Presentations

Variation in community structure is mediated by interactions between species traits and a site's environmental characteristics. Previously, data on community composition at sites has been employed to correlate trait and environmental variables (e.g., RLQ analysis) and to predict community-level expression of quantitative traits (i.e., community aggregated traits). Here, we demonstrate that the selection ratio, a method originating in animal resource selection studies, can estimate the ecological filters that site conditions impose on species traits by combining observed community aggregated traits with null models of species availability. This flexible, nonparametric approach expresses the filter at each site as a probability density …

Mitochondrial Inheritance And Natural Phenotypic Variation Among Caenorhabditis Briggsae Populations, Anna Luella Coleman-Hulbert

Dissertations and Theses

Mutations affecting the mitochondrial electron transport chain cause numerous neurodegenerative disorders in humans and affect longevity in other organisms. A natural model system to study the relationship between mitochondrial function and aging within an evolutionary or population genetic context has been lacking. Natural populations of Caenorhabditis briggsae nematodes were recently found to harbor mitochondrial genetic variation with likely functional consequences for aging. Specifically, C. briggsae isolates containing high frequencies of a deletion mutation affecting the mitochondrial NADH dehydrogenase 5 (ND5) gene were found to have reduced reproductive fitness and lifespan and elevated levels of mutagenic superoxide. Here, rates …

Mitochondrial Physiology Of Diapausing And Developing Embryos Of The Annual Killifish Austrofundulus Limnaeus: Implications For Extreme Anoxia Tolerance, Jeffrey M. Duerr, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Diapausing embryos of the annual killifish Austrofundulus limnaeus have the highest reported anoxia tolerance of any vertebrate and previous studies indicate modified mitochondrial physiology likely supports anoxic metabolism. Functional mitochondria isolated from diapausing and developing embryos of the annual killifish exhibited VO2, respiratory control ratios (RCR), and P:O ratios consistent with those obtained from other ectothermic vertebrate species. Reduced oxygen consumption associated with dormancy in whole animal respiration rates are correlated with maximal respiration rates of mitochondria isolated from diapausing versus developing embryos. P:O ratios for developing embryos were similar to those obtained from adult liver, but were diminished in …

The Isolation Of Viruses Infecting Archaea, Kenneth M. Stedman, Kate Porter, Mike L. Dyall-Smith

Biology Faculty Publications and Presentations

A mere 50 viruses of Archaea have been reported to date; these have been investigated mostly by adapting methods used to isolate bacteriophages to the unique growth conditions of their archaeal hosts. The most numerous are viruses of thermophilic Archaea. These viruses have been discovered by screening enrichment cultures and novel isolates from environmental samples for their ability to form halos of growth inhibition, or by using electron microscopy to screen enrichment cultures for virus-like particles. Direct isolation without enrichment has not yet been successful for viruses of extreme thermophiles. On the other hand, most viruses of extreme halophiles, the …

Spatial Segregation Of The Sexes In A Salt Marsh Grass Distichlis Spicata (Poaceae), Charlene Ashley Mercer

Dissertations and Theses

Understanding the maintenance of sexual systems is of great interest to evolutionary and ecological biologists because plant systems are extremely varied. Plant sexual systems have evolved to include not only complete plants with both male and female reproduction occurring on one plant (i.e., monoecious and hermaphroditic) but also plants with male and female function on separate plants (dioecious). The dioecious reproductive system can be used to test theories on niche differentiation given that having separate plants potentially allows for the exploitation of a broader niche. This increase in the realized niche is due to the ability for separate sexes to …

Phylogeographic Patterns And Intervarietal Relationships Within Lupinus Lepidus: Morphological Differences, Genetic Similarities, Kevin Allen Weitemier

Dissertations and Theses

Lupinus lepidus (Fabaceae) contains many morphologically divergent varieties and was restricted in its range during the last period of glaciation. A combination of phylogenetic (with the trnDT and LEGCYC1A loci) and population genetics approaches (with microsatellites and LEGCYC1A are used here to characterize intervarietal relationships and examine hypotheses of recolonization of areas in the Pacific Northwest affected by glaciation. Sequenced loci are not found to form a clade exclusive to L. lepidus, nor are any of the varieties found to form clades. Population genetics analyses reveal only negligible genetic structure within L. lepidus, with the majority of variation …

A Phylogenetic Study Of The Old World Asclepiadinae (Apocynaceae) Based On Chloroplast And Nuclear Dna Sequence Data, David Chuba

Dissertations and Theses

Relationships within the African Asclepias generic complex (Asclepiadinae, Apocynaceae) have for a long time been only a matter of intuitive speculation and generic delimitations have been diverse and rather contentious. Generic delimitation in this group has been based on morphological characters that are usually not exclusive to any particular clade or genus. The difficulty of identifying taxonomically useful morphological characters for inferring generic delimitations has led to differences in the emphasized characters by different taxonomists. This study is aimed at understanding phylogenetic relationships of species within the African Asclepias complex based upon the nuclear PgiC and three chloroplast DNA regions, …