Biology Commons^™

Multiple Acquisitions Of Pathogen-Derived Francisella Endosymbionts In Soft Ticks, Jonathan G. Gerhart, H. Auguste Dutcher, Amanda E. Brenner, Abraham S. Moses, Libor Grubhoffer, Rahul Raghavan

Biology Faculty Publications and Presentations

Bacterial endosymbionts of ticks are of interest due to their close evolutionary relationships with tick-vectored pathogens. For instance, whereas many ticks contain Francisella-like endosymbionts (FLEs), others transmit the mammalian pathogen Francisella tularensis. We recently sequenced the genome of an FLE present in the hard tick Amblyomma maculatum (FLE-Am) and showed that it likely evolved from a pathogenic ancestor. In order to expand our understanding of FLEs, in the current study we sequenced the genome of an FLE in the soft tick Ornithodoros moubata and compared it to the genomes of FLE-Am, Francisella persica—an FLE in the soft tick Argus (Persicargas) …

Baseline Mrna Expression Differs Widely Between Common Laboratory Strains Of Zebrafish, Lindsay Holden, Kim H. Brown

Biology Faculty Publications and Presentations

Common strains of wildtype zebrafish (Danio rerio) have unique genomic features including SNPs and CNV, but strain information often goes unreported in the literature. As a result, the confounding effects of interstrain variation makes repetition of studies in zebrafish challenging. Here we analyze hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen (TU), and WIK) using Agilent 4 × 44 K gene expression microarrays to establish baseline mRNA expression across strains and between sexes. We observed wide variation in sex-specific gene expression within AB and WIK strains (141 genes in AB and 67 genes in WIK), …

Identification Of Novel Mites (Miniature Inverted-Repeat Transposable Elements) In Coxiella Burnetii: Implications For Protein And Small Rna Evolution, Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F. Minnick

Biology Faculty Publications and Presentations

Background: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. Results: We describe two MITE families discovered during research on small non-coding …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses—which infect members of the order Sulfolobales, growing optimally at 80 C and pH 3—are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. Nonetheless, much remains to be learned about these viruses. In order to investigate fusellovirus evolution, we have isolated and characterized a novel fusellovirus, Sulfolobus spindle-shaped virus 10 (formerly SSV-L1). Comparative genomic analyses highlight significant similarity with both SSV8 and SSV9, as well as conservation of promoter elements within the Fuselloviridae. SSV10 encodes five ORFs with no …

Connecting Chemistry To Community With Deliberative Democracy, Regis Komperda, Jack Barbera, Erin Shortlidge, Gwen Shusterman, Stem Education And Equity Institute, Portland State University

Biology Faculty Publications and Presentations

Science education communities have called for rethinking curricula to improve student understanding of the nature of science and the role of science in addressing controversial modern issues such as climate change, energy policy, and pollution levels. One approach to meeting this call is integrating these topics into class activities that require students to use discussion and scientific approaches to solve problems and deliberate potential policy solutions. Deliberative democracy (DD) is one such active learning approach in which students work in peer groups to reach a consensus on a scientific topic relevant to both real-world issues and course content. During DD …

Genome-Wide Screening Of Potential Rnase Y-Processed Mrnas In The M49 Serotype Streptococcus Pyogenes Nz131, Zhiyun Chen, Rahul Raghavan, Fengxia Qi, Justin Merritt, Jens Kreth

Biology Faculty Publications and Presentations

RNase Y is a major endoribonuclease in Group A streptococcus (GAS) and other Gram‐positive bacteria. Our previous study showed that RNase Y was involved in mRNA degradation and processing in GAS. We hypothesized that mRNA processing regulated the expression of important GAS virulence factors via altering their mRNA stabilities and that RNase Y mediated at least some of the mRNA‐processing events. The aims of this study were to (1) identify mRNAs that were processed by RNase Y and (2) confirm the mRNA‐processing events. The transcriptomes of Streptococcus pyogenes NZ131 wild type and its RNase Y mutant (Δrny) were …

Feather Mite Abundance Varies But Symbiotic Nature Of Mite-Host Relationship Does Not Differ Between Two Ecologically Dissimilar Warblers, Alix E. Matthews, Jeffery L. Larkin, Douglas W. Raybuck, Morgan C. Slevin, Scott H. Stoleson, Than J. Boves

Biology Faculty Publications and Presentations

Feather mites are obligatory ectosymbionts of birds that primarily feed on the oily secretions from the uropygial gland. Feather mite abundance varies within and among host species and has various effects on host condition and fitness, but there is little consensus on factors that drive variation of this symbiotic system. We tested hypotheses regarding how within-species and among-species traits explain variation in both (1) mite abundance and (2) relationships between mite abundance and host body condition and components of host fitness (reproductive performance and apparent annual survival). We focused on two closely related (Parulidae), but ecologically distinct, species: Setophaga cerulea …

Genetic Analysis Of The Major Capsid Protein Of The Archaeal Fusellovirus Ssv1: Mutational Flexibility And Conformational Change, Eric A. Iverson, David A. Goodman, Madeline E. Gorchels, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses with spindle or lemon-shaped virions are rare in the world of viruses, but are common in viruses of archaeal extremophiles, possibly due to the extreme conditions in which they thrive. However, the structural and genetic basis for the unique spindle shape is unknown. The best-studied spindle-shaped virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), is composed mostly of the major capsid protein VP1. Similar to many other viruses, proteolytic cleavage of VP1 is thought to be critical for virion formation. Unlike half of the genes in SSV1, including the minor capsid protein gene VP3, the VP1 gene does not tolerate …

Flushing Responses Of Golden Eagles (Aquila Chrysaetos) In Response To Recreation, Robert J. Spaul, Julie A. Heath

Biology Faculty Publications and Presentations

Disturbance because of human activity, including recreation on wildlands, can affect bird behavior which in turn can reduce breeding success, an important consideration for species of management concern. We observed Golden Eagles (Aquila chysaetos) during the breeding season to determine whether the probability of flushing was affected by the type of recreationist, distance to encounter, eagle nest attendance, or date. We monitored eagles in 23 nesting territories from distant (600-1,200 m) observation points and recorded recreation activity within 1,200 m of eagles in the Owyhee Front of southwestern Idaho. In most (86%, n = 270) encounters, eagles did …

Commentary: Research Recommendations For Understanding The Decline Of American Kestrels (Falco Sparverius) Across Much Of North America, Christopher J.W. Mcclure, Sarah E. Schulwitz, Richard Van Buskirk, Benjamin P. Pauli, Julie A. Heath

Biology Faculty Publications and Presentations

Across much of North America, populations of American Kestrels (Falco sparverius) have been in decline for decades (Farmer et al. 2008, Farmer and Smith 2009, Smallwood et al. 2009a, Paprocki et al. 2014, Sauer et al. 2014). Hypothesized causes of kestrel declines include predation by Cooper's Hawks (Accipiter cooperii; Farmer et al. 2008), pathogens (e.g., Nemeth et al. 2006), habitat loss (Sullivan and Wood 2005, Farmer et al. 2008, Bolgiano et al. 2015), pesticides (Smallwood et al. 2009a, Rattner et al. 2015), and climate change (Steenhof and Peterson 2009b), yet no hypothesized factor has been supported …

Dynamics Of Prochlorococcus And Synechococcus At Station Aloha Revealed Through Flow Cytometry And High-Resolution Vertical Sampling, Ger J. Van Den Engh, Joseph K. Doggett, Anne W. Thompson, Martina A. Doblin, Carla N.G. Gimpel, David M. Karl

Biology Faculty Publications and Presentations

The fluorescence and scattering properties of Prochlorococcus and Synechococcus at Station ALOHA as measured by flow cytometry (termed the FCM phenotype) vary with depth and over a variety of time scales. The variation in FCM phenotypes may reflect population selection or physiological acclimation to local conditions. Observations before, during, and after a storm with deep water mixing show a short-term homogenization of the FCM phenotypes with depth, followed by a return to the stable pattern over the time span of a few days. These dynamics indicate that, within the upper mixed-layer, the FCM phenotype distribution represents acclimation to ambient light. …

A Metabolic Hypothesis For The Evolution Of Temperature Effects On The Arterial Pco2 And Ph Of Vertebrate Ectotherms, Stanley S. Hillman, Michael Scott Hedrick

Biology Faculty Publications and Presentations

Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in temperature. This ‘alphastat’ pH pattern has previously been interpreted as being evolutionarily-driven by the maintenance of a constant protonation state on the imidazole moiety of histidine protein residues, hence stabilizing protein structure-function. Analysis of the existing data for interclass responses of ectothermic vertebrates show different degrees of PaCO2 increases and pH declines with temperature between the classes with reptiles>amphibians>fish. The PaCO2 at the temperature where maximal aerobic metabolism (VO2max) …

An Efficient Pipeline To Generate Data For Studies In Plastid Population Genomics And Phylogeography, Brendan F. Kohrn, Jessica M. Persinger, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Premise of the study: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole‐genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single‐nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure.

Methods: We developed sampling methodologies and an application, CallHap, that uses a least‐squares algorithm to evaluate the fit between …

The Landscape Of Mtdna Modifications In Cancer: A Tale Of Two Cities, Kate L. Hertweck, Santanu Dasgupta

Biology Faculty Publications and Presentations

Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional implications of mitochondrial mutations in cancer, this article focuses on documenting current knowledge in the abundance and distribution of somatic mitochondrial mutations, followed by elucidation of processes which affect the fate of mutations in cancer cells. The conclusion includes an overview of translational implications for mtDNA mutations, as well as recommendations for future research uniting mitochondrial variants and tumorigenesis.

Alectryon Vitiensis: A New Species Of Sapindaceae Endemic To Fiji, Sven Buerki, Porter P. Lowry Ii, Jérôme Munzinger, Marika Tuiwawa, Alivereti Naikatini, Martin W. Callmander

Biology Faculty Publications and Presentations

A new species of Alectryon Gaertn. (Sapindaceae) endemic to the Fijian archipelago is described as A. vitiensis Buerki, Lowry, Munzinger & Callm. based on morphological and molecular evidence. It can easily be distinguished from the two congeners currently known from Fiji by its smaller leaves, subsessile leaflets, apetalous flowers, and crested fruits. A phylogenetic analysis using ITS sequence data shows that the new species is closely related to two Australian endemics, A. diversifolius (F. Muell.) S. T. Reynolds and A. oleifolius (Desf.) S. T. Reynolds, but differs in having compound leaves covered with a golden indument. Moreover, the Australian taxa …

Case Report: Coincidental Inclusion In A 17-Locus Y-Str Mixture, Wrongful Conviction And Exoneration, Greg Hampikian, Gianluca Peri, Shih-Shiang Lo, Mon-Hwa Chin, Kuo-Lan Liu

Biology Faculty Publications and Presentations

We report the case of a suspect (Suspect-3) who was convicted (and later exonerated) of participating in the multiple-attacker rape of two women. The forensic evidence against him was his inclusion in a 17-marker Y-STR mixture isolated from semen on one victim’s clothing. The DNA inclusion produced a match statistic with a combined probability of inclusion of 1 in 741, and a Likelihood Ratio of 3296. While the defense team was told that Suspect-3 was included in the semen DNA mixture, they were not told that all of the Y-STR alleles could also be explained by just the other two …

Fatal Attraction?: Intraguild Facilitation And Suppression Among Predators, Kelly J. Sivy, Casey B. Pozzanghera, James B. Grace, Laura R. Prugh

Biology Faculty Publications and Presentations

Competition and suppression are recognized as dominant forces that structure predator communities. Facilitation via carrion provisioning, however, is a ubiquitous interaction among predators that could offset the strength of suppression. Understanding the relative importance of these positive and negative interactions is necessary to anticipate community-wide responses to apex predator declines and recoveries worldwide. Using state-sponsored wolf (Canis lupus) control in Alaska as a quasi experiment, we conducted snow track surveys of apex, meso-, and small predators to test for evidence of carnivore cascades (e.g., mesopredator release). We analyzed survey data using an integrative occupancy and structural equation modeling …

Plasma Cell Survival In The Absence Of B Cell Memory, Erika Hammarlund, Archana Thomas, Ian J. Amanna, Lindsay Holden, Ov D. Slayden, Byung S. Park, Lina Gao, Mark K. Slifka

Biology Faculty Publications and Presentations

Pre-existing serum antibodies play an important role in vaccine-mediated protection against infection but the underlying mechanisms of immune memory are unclear. Clinical studies indicate that antigen-specific antibody responses can be maintained for many years, leading to theories that reactivation/differentiation of memory B cells into plasma cells is required to sustain long-term antibody production. Here, we present a decade-long study in which we demonstrate site-specific survival of bone marrow-derived plasma cells and durable antibody responses to multiple virus and vaccine antigens in rhesus macaques for years after sustained memory B cell depletion. Moreover, BrdU+ cells with plasma cell morphology can be …

Adaptive Evolution Under Extreme Genetic Drift In Oxidatively Stressed Caenorhabditis Elegans, Stephen Fuller Christy, Riana I. Wernick, Michael James Lue, Griselda Velasco, Dana K. Howe, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that …

Use Of Gene Editing In Usda Research, Mark R. Mclellan, Patsy Brannon, Adriana Campa, Carrie Castille, Steven Daley-Laursen, Roch Gaussoin, Govind Kannan, Mark Lawrence, Dawn Thilmany

Biology Faculty Publications and Presentations

The Science Advisory Council was established in FY2016 as a subcommittee of the National Agricultural Research, Extension, Education, and Economics (NAREEE) Advisory Board by the Chief Scientist as a result of recommendations from the 2012 report on Agricultural Preparedness by the President’s Council of Advisors on Science and Technology. The Council's charge is to provide advice and guidance, on a scientific basis, on the overall strength, practicality, and direction of agricultural research, including emerging technology and scientific issues and report any findings publicly to the NAREEE Advisory Board.

The USDA Chief Scientist first asked the Council to examine rigor and …

Efficacy Of Neutral And Negatively Charged Liposome-Loaded Gentamicin On Planktonic Bacteria And Biofilm Communities, Moayad Alhariri, Majad A. Majrashi, Ali H. Bahkali, Faisal S. Almajed, Ali Azghani, Mohammed A. Khiyami, Essam J. Alyamani, Sameera M. Aljohani, Majed A. Halwani

Biology Faculty Publications and Presentations

We investigated the efficacy of liposomal gentamicin formulations of different surface charges against Pseudomonas aeruginosa and Klebsiella oxytoca. The liposomal gentamicin formulations were prepared by the dehydration-rehydration method, and their sizes and zeta potential were measured. Gentamicin encapsulation efficiency inside the liposomal formulations was determined by microbiologic assay, and stability of the formulations in biologic fluid was evaluated for a period of 48h. The minimum inhibitory concentration and the minimum bactericidal concentration were determined, and the in vitro time kill studies of the free form of gentamicin and liposomal gentamicin formulations were performed. The activities of liposomal gentamicin in preventing …

Natural History Collections: Teaching About Biodiversity Across Time, Space, And Digital Platforms, Anna K. Monfils, Karen E. Powers, Christopher J. Marshall, Christopher T. Martine, James F. Smith, L. Alan Prather

Biology Faculty Publications and Presentations

Natural history collections offer unique physical and virtual opportunities for formal and informal progressive learning. Collections are unique data in that they each represent a biological record at a single place and time that cannot be obtained by any other method. Collections-based experiences lead to an increased understanding of and substantive interaction with the living world. Global biological diversity and changes in that diversity are directly tracked through specimens in collections, regardless of whether changes are ancient or recent. We discuss how collections, specimens, and the data associated with them, can be critical components linking nature and scientific inquiry. Specimens …

Winter Diet Of Bobolink, A Long-Distance Migratory Grassland Bird, Inferred From Feather Isotopes, Rosalind B. Renfrew, Jason M. Hill, Daniel H. Kim, Christopher Romanek, Noah G. Perlut

Biology Faculty Publications and Presentations

Effective conservation of migratory bird populations depends on advancements in our understanding of processes throughout the life cycle. Fundamental information about wintering ecology (e.g., habitat use and diet composition) remains limited, which limits assessment of threats to populations during winter. Bobolink (Dolichonyx oryzivorus) is a year-round grassland obligate and Nearctic-Neotropical migrant that undergoes 2 complete molts each year, including a complete prealternate molt on the South American wintering grounds. This unusual winter molt provides a rare opportunity to examine, using stable isotope analysis, the timing and contribution of foraging resources in the Bobolink diet prior to northbound migration from disparate …

Arginine Vasotocin And Neuropeptide Y Vary With Seasonal Life-History Transitions In Garter Snakes, Ashley R. Lucas, Daelyn Y. Richards, Lucy M. Ramirez, Deborah Lutterschmidt

Biology Faculty Publications and Presentations

Transitions between life-history stages are often accompanied by dramatic behavioral switches that result from a shift in motivation to pursue one resource over another. While the neuroendocrine mechanisms that regulate such behavioral transitions are poorly understood, arginine vasotocin (AVT) and neuropeptide Y (NPY) are excellent candidates because they modulate reproductive and feeding behavior, respectively. We asked if seasonal changes in AVT and NPY are concomitant with the seasonal migration to and from the feeding grounds in red-sided garter snakes (Thamnophis sirtalis parietalis). Male and female snakes were collected in different migratory states during both the spring and fall. The total …

Counterintuitive Roles Of Experience And Weather On Migratory Performance, Adrian I. Rus, Adam E. Duerr, Tricia A. Miller, James R. Belthoff, Todd Katzner

Biology Faculty Publications and Presentations

Migration allows animals to live in resource-rich but seasonally variable environments. Because of the costs of migration, there is selective pressure to capitalize on variation in weather to optimize migratory performance. To test the degree to which migratory performance (defined as speed of migration) of Golden Eagles (Aquila chrysaetos) was determined by age- and season-specific responses to variation in weather, we analyzed 1,863 daily tracks (n = 83 migrant eagles) and 8,047 hourly tracks (n = 83) based on 15 min GPS telemetry data from Golden Eagles and 277 hourly tracks based on 30 s data …

Correlates Of Immune Defenses In Golden Eagle Nestlings, Benjamin M. Dudek, Julie A. Heath

Biology Faculty Publications and Presentations

An individual’s investment in constitutive immune defenses depends on both intrinsic and extrinsic factors. We examined how Leucocytozoon parasite presence, body condition (scaled mass), heterophil-to-lymphocyte (H:L) ratio, sex, and age affected immune defenses in golden eagle (Aquila chrysaetos) nestlings from three regions: California, Oregon, and Idaho. We quantified hemolytic-complement activity and bacterial killing ability, two measures of constitutive immunity. Body condition and age did not affect immune defenses. However, eagles with lower H:L ratios had lower complement activity, corroborating other findings that animals in better condition sometimes invest less in constitutive immunity. In addition, eagles with Leucocytozoon infections had higher …

Simulations Reveal The Power And Peril Of Artificial Breeding Sites For Monitoring And Managing Animals, Christopher J.W. Mcclure, Benjamin P. Pauli, Julie A. Heath

Biology Faculty Publications and Presentations

Despite common use, the efficacy of artificial breeding sites (e.g., nest boxes, bat houses, artificial burrows) as tools for monitoring and managing animals depends on the demography of target populations and availability of natural sites. Yet, the conditions enabling artificial breeding sites to be useful or informative have yet to be articulated. We use a stochastic simulation model to determine situations where artificial breeding sites are either useful or disadvantageous for monitoring and managing animals. Artificial breeding sites are a convenient tool for monitoring animals and therefore occupancy of artificial breeding sites is often used as an index of population …

Forecasting Disturbance Effects On Wildlife: Tolerance Does Not Mitigate Effects Of Increased Recreation On Wild Lands, B. P. Pauli, R. J. Spaul, J. A. Heath

Biology Faculty Publications and Presentations

There is widespread evidence that human disturbance affects wildlife behavior, but long-term population effects can be difficult to quantify. Individual-based models (IBMs) offer a way to assess population-level, aggregate effects of disturbance on wildlife. We created TRAILS (Tolerance in Raptors and the Associated Impacts of Leisure Sports), an IBM that simulates interactions between recreationists and nesting raptors, to assess the effect of human disturbance on raptor populations and test if changes in tolerance to disturbance could mitigate negative consequences. We used behavioral and demographic data from golden eagles (Aquila chrysaetos), and recreation activity data to parameterize TRAILS and …

Experimental Evolution With Caenorhabditis Nematodes, Henrique Teotónio, Suzanne Estes, Patrick C. Phillips, Charles F. Baer

Biology Faculty Publications and Presentations

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic …

Horizontally Acquired Biosynthesis Genes Boost Coxiella Burnetii's Physiology, Abraham S. Moses, Jess A. Millar, Matteo Bonazzi, Paul A. Beare, Rahul Raghavan

Biology Faculty Publications and Presentations

Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella-like bacteria found in ticks. Horizontally acquired genes that …