Biology Commons^™

New Implications On Genomic Adaptation Derived From The Helicobacter Pylori Genome Comparison, Edgar Eduardo Lara-Ramírez, Aldo Segura-Cabrera, Xianwu Guo, Gongxin Yu, Carlos Armando García-Pérez, Mario A. Rodríguez-Pérez

Biology Faculty Publications and Presentations

Background: Helicobacter pylori has a reduced genome and lives in a tough environment for long-term persistence. It evolved with its particular characteristics for biological adaptation. Because several H. pylori genome sequences are available, comparative analysis could help to better understand genomic adaptation of this particular bacterium.

Principal Findings: We analyzed nine H. pylori genomes with emphasis on microevolution from a different perspective. Inversion was an important factor to shape the genome structure. Illegitimate recombination not only led to genomic inversion but also inverted fragment duplication, both of which contributed to the creation of new genes and gene family, and further, …

Migration Patterns, Use Of Stopover Areas, And Austral Summer Movements Of Swainson's Hawks, Michael N. Kochert, Mark R. Fuller, Linda S. Schueck, Laura Bond, Marc J. Bechard, Brian Woodbridge, Geoff L. Holroyd, Mark S. Martell, Ursula Banasch

Biology Faculty Publications and Presentations

From 1995 to 1998, we tracked movements of adult Swainson’s Hawks (Buteo swainsoni), using satellite telemetry to characterize migration, important stopover areas, and movements in the austral summer. We tagged 46 hawks from July to September on their nesting grounds in seven U.S. states and two Canadian provinces. Swainson’s Hawks followed three basic routes south on a broad front, converged along the east coast of central Mexico, and followed a concentrated corridor to a communal area in central Argentina for the austral summer. North of 20°N, southward and northward tracks differed little for individuals from east of the …

Labile Soil Carbon Inputs Mediate The Soil Microbial Community Composition And Plant Residue Decomposition Rates, Marie-Anne De Graaff, Aimee T. Classen, Hector F. Castro, Christopher W. Schadt

Biology Faculty Publications and Presentations

• Root carbon (C) inputs may regulate decomposition rates in soil, and in this study we ask: how do labile C inputs regulate decomposition of plant residues, and soil microbial communities?

• In a 14 d laboratory incubation, we added C compounds often found in root exudates in seven different concentrations (0, 0.7, 1.4, 3.6, 7.2, 14.4 and 21.7 mg C g soil) to soils amended with and without ¹³C-labeled plant residue. We measured CO₂ respiration and shifts in relative fungal and bacterial rRNA gene copy numbers using quantitative polymerase chain reaction (qPCR).

• Increased labile C input …

A Comparison Of Cumulative-Germination Response Of Cheatgrass (Bromus Tectorum L.) And Five Perennial Bunchgrass Species To Simulated Field-Temperature Regimes, Stuart P. Hardegree, Corey A. Moffet, Bruce A. Roundy, Thomas A. Jones, Stephen J. Novak, Patrick E. Clark, Frederick B. Pierson, Gerald N. Flerchinger

Biology Faculty Publications and Presentations

Cheatgrass (Bromus tectorum L.) has come to dominate millions of hectares of rangeland in the Intermountain western United States. Previous studies have hypothesized that one mechanism conferring a competitive advantage to this species is the ability to germinate rapidly at low temperatures in the fall, winter and spring and, therefore, initiate growth and establishment more rapidly than more desirable perennial bunchgrass species. In this experiment, we developed thermal-germination-response models for multiple seedlots of cheatgrass and five perennial grass species. We conducted sensitivity analysis on potentialcumulative- germination response to a 38-y simulation of field-variable conditions of seedbed temperature and moisture. …

Eighteen Microsatellite Loci Developed From Western Burrowing Owls (Athene Cunicularia Hypugaea), Brant C. Faircloth, Alexandra Title, Kevin Tan, Justin Welty, James R. Belthoff, Patricia Adair Gowaty

Biology Faculty Publications and Presentations

Western burrowing owls (Athene cunicularia hypugaea) are ground-dwelling owls distributed throughout western North America. Because of population declines, this species is considered endangered in Canada, and burrowing owls are listed as a species of conservation concern in states of the western USA. Korfanta et al. (2002) previously presented primers for seven microsatellite loci in burrowing owls. Parentage and relatedness studies require a larger number of markers for accuracy and precision. Here, we developed and characterized 18 additional microsatellite DNA loci, and we tested these loci in 23 individuals. The number of alleles per locus ranged from 2 to …

The Role Of Caspases In Alzheimer's Disease; Potential Novel Therapeutic Opportunities, Troy T. Rohn

Biology Faculty Publications and Presentations

Although apoptosis plays a critical role in molding the CNS into its final appearance and function, inappropriate activation of this pathway in the aging brain may contribute to neurodegeneration. In Alzheimer’s disease (AD), an overwhelming body of evidence supports the activation of apoptosis in general, and caspases specifically as an early event that may not only contribute to neurodegeneration but also promote the underlying pathology associated with this disease. Therefore, caspase inhibitors may provide an effective strategy for treating AD. However, despite the compelling evidence indicating a role for caspases in disease progression, chronic treatment with caspase inhibitors in animal …

Non-Native Salmonids Affect Amphibian Occupancy At Multiple Spatial Scales, David S. Pilliod, Blake R. Hossack, Peter F. Bahls, Evelyn L. Bull, Paul Stephen Corn, Grant Hokit, Bryce A. Maxell, James C. Munger, Aimee Wyrick

Biology Faculty Publications and Presentations

Aim The introduction of non-native species into aquatic environments has been linked with local extinctions and altered distributions of native species. We investigated the effect of non-native salmonids on the occupancy of two native amphibians, the long-toed salamander (Ambystoma macrodactylum) and Columbia spotted frog (Rana luteiventris), across three spatial scales: water bodies, small catchments and large catchments.

Location Mountain lakes at ≥ 1500 m elevation were surveyed across the northern Rocky Mountains, USA.

Methods We surveyed 2267 water bodies for amphibian occupancy (based on evidence of reproduction) and fish presence between 1986 and 2002 and modelled …

GenHtr: A Tool For Comparative Assessment Of Genetic Heterogeneity In Microbial Genomes Generated By Massive Short-Read Sequencing, Gongxin Yu

Biology Faculty Publications and Presentations

Background: Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome …

Foraging Strategies Are Related To Skull Morphology And Life History Traits Of Melanerpes Woodpeckers, David L. Leonard Jr., Julie A. Heath

Biology Faculty Publications and Presentations

Links between morphology and foraging strategies have been well established for many vertebrate groups. Foraging strategies of Melanerpes woodpeckers are especially variable, with at least six species being proficient flycatchers; the remainder of the better known species do not flycatch. Our objective was to examine variation in foraging tactics as it relates to skull morphology and other life history traits among these species to better understand the biology of these diverse woodpeckers. We measured eight skull characters from 241 individuals representing 19 species, but focused on eight species for which we had the most data. We used the log-geometric mean …

Agolohymena Aspidocauda Nov. Gen., Nov. Spec., A Histophagous Freshwater Tetrahymenid Ciliate In The Family Deltopylidae (Ciliophora, Hymenostomatia), From Idaho (Northwest U.S.A.): Morphology, Ontogenesis And Molecular Phylogeny, William A. Bourland, Michaela C. Strüder-Kypke

Biology Faculty Publications and Presentations

Morphology, ontogeny and the molecular phylogeny of Agolohymena aspidocauda nov. gen., nov. spec., a new freshwater tetrahymenid ciliate from Idaho, U.S.A, are described. The ontogeny and histophagous mode of nutrition are similar to those of Deltopylum rhabdoides Fauré-Fremiet and Mugard, 1946. The new genus is placed with Deltopylum in the resurrected family Deltopylidae Song & Wilbert, 1989. We emend the diagnostic features of the family to include division by polytomy, right and left somatic kineties extending into the preoral suture, crook-shaped or sigmoid adoral membranelles 1 and 2, markedly reduced adoral membranelle 3 and a tetrahymenid silverline pattern. The main …

Effects Of Old Nest Material On Occupancy And Reuse Of Artificial Burrows, And Breeding Dispersal By Burrowing Owls (Athene Cunicularia) In Southwestern Idaho, Corey S. Riding

Boise State University Theses and Dissertations

This thesis comprises two chapters describing my investigations of the breeding ecology of burrowing owls (Athene cunicularia) in southwestern Idaho. The first chapter details two experimental studies where I examined the effects of old nest material, primarily mammal dung, on the occupancy and reuse of artificial burrows by burrowing owls in 2004 and 2005. For burrows that owls had not used previously for nesting, adding material from actual nests did not induce occupancy. Thus, old nest material does not appear to function as a cue for burrow suitability. Removing old material from burrows that owls had used for …

Present Effects Of Past Wildfires On Leaf Litter Breakdown In Stream Ecosystems, Peter Koetsier, Teresa R. B. Krause, Quenton M. Tuckett

Biology Faculty Publications and Presentations

We investigated the present effects from a 10-year-old wildfire on leaf litter breakdown rates in 3 headwater streams in central Idaho. These systems experienced a massive debris flow one year after the fire. Based on soil instability and burn patterns, we identified 3 stream conditions: unburned, burned only, and burned/scoured. We placed leaf bags containing willow leaves (Salix sp.) in each stream type and removed bags at various time intervals until all bags were collected 100 days after their introduction. Leaf material was dried and weighed, and decay rate coefficients were calculated. Macroinvertebrates colonizing the bags were enumerated and identified, …

Caspase-Cleaved Tar Dna-Binding Protein-43 In Parkinson’S Disease And Dementia With Lewy Bodies, Polina Kokoulina, Troy T. Rohn

Biology Faculty Publications and Presentations

Background: TAR DNA-binding protein-43 (TDP-43) proteinopathies are classified based upon the extent of modified TDP-43 and include a growing number of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with ubiquitin immunoreactive, tau-negative inclusions (FTLD-U) and FTLD with motor neuron disease (FTLD-MND). Objective: The purpose of the study was to examine whether proteolytic modifications of TDP-43 are a relevant finding in Parkinson’s disease (PD) and dementia with Lewy Bodies (DLB). Methods: A novel site-directed caspase-cleavage antibody, termed TDP caspase-cleavage product antibody (TDPccp), was utilized based upon a known caspase-3 cleavage consensus site within TDP-43 at position 219. …

Biology Of Cancer Class Metastasizes Knowledge, Chris Barbey, Madeline Connley, Ben Davis, Rachel Hightower, Jon Reeck, Caleb Sutherland, Cheryl L. Jorcyk

Service-Learning Program

Cancer, in all its forms, is a leading cause of death and serious disease. The pathology of cancer is very complicated. This combined with the fast pace of research and clinical innovation makes cancer biology a difficult topic, even for experts. As a consequence, patients who wish to gain a better understanding of cancer biology may find themselves stuck somewhere between the blog-a-sphere and technical journals. Cancer is a disease of miscommunication and confusion at the level of cellular signaling. In a sense, this theme of confusion extends to the experience of the patient. The body is in rebellion, perhaps …

Effects Of Small Increases In Corticosterone Levels On Morphology, Immune Function, And Feather Development, Michael W. Butler, Lynda L. Leppert, Alfred M. Dufty Jr.

Biology Faculty Publications and Presentations

Stressors encountered during avian development may affect an individual’s phenotype, including immunocompetence, growth, and feather quality. We examined effects of simulated chronic low-level stress on American kestrel (Falco sparverius) nestlings. Continuous release of corticosterone, a hormone involved in the stress response, can model chronic stress in birds. We implanted 13-d-old males with either corticosterone-filled implants or shams and measured their growth, immune function, and feather coloration.We found no significant differences between groups at the end of the weeklong exposure period in morphometrics (mass, tarsus, wing length, and asymmetry), immunocompetence (cutaneous immunity, heterophil/lymphocyte ratio, and humoral immunity), or feather …

Phenotypic Divergence During The Invasion Of Phyla Canescens In Australia And France: Evidence For Selection-Driven Evolution, Cheng-Yuan Xu, Mic H. Julien, Mohammad Fatemi, Christophe Girod, Rieks D. Van Klinken, Caroline L. Gross, Stephen J. Novak

Biology Faculty Publications and Presentations

Rapid adaptive evolution has been advocated as a mechanism that promotes invasion. Demonstrating adaptive evolution in invasive species requires rigorous analysis of phenotypic shifts driven by selection. Here, we document selection-driven evolution of Phyla canescens, an Argentine weed, in two invaded regions (Australia and France). Invasive populations possessed similar or higher diversity than native populations, and displayed mixed lineages from different sources, suggesting that genetic bottlenecks in both countries might have been alleviated by multiple introductions. Compared to native populations, Australian populations displayed more investment in sexual reproduction, whereas French populations possessed enhanced vegetative reproduction and growth. We partitioned …

American Kestrel Reproduction: Evidence For The Selection Hypothesis And The Role Of Dispersal, Karen Steenhof, Julie A. Heath

Biology Faculty Publications and Presentations

Many hypotheses attempt to explain why younger, less experienced birds have relatively low reproductive output. We evaluated reproductive patterns of marked American Kestrels Falco sparverius nesting in boxes in southwestern Idaho from 1992 to 2006 to test predictions of these hypotheses. Results were consistent with the selection (differential mortality) hypothesis and did not support the constraint, restraint or recruitment hypotheses. Most known-age Kestrels nested in their first year of life, and there was no apparent short-term or long-term reproductive advantage to delayed breeding. The number of years that Kestrels nested in study area boxes ranged from 1 to 6 years, …

Environmental Regulation Of Dormancy Loss In Lomatium Dissectum (Apiaceae) Seeds, Melissa Scholten, Jacklyn Donahue, Nancy L. Shaw, Marcelo Serpe

Biology Faculty Publications and Presentations

Background and aims Lomatium dissectum (Apiaceae) is a perennial, herbaceous plant of wide distribution in Western North America. At the time of dispersal, L. dissectum seeds are dormant and have underdeveloped embryos. The aims of this work were to determine the requirements for dormancy break and germination, to characterize the type of seed dormancy, and to determine the effect of dehydration after embryo growth on seed viability and secondary dormancy.

Methods The temperature requirements for embryo growth and germination were investigated under growth chamber and field conditions. The effect of GA3 on embryo growth was also analyzed to determine the …

Seed Predation On Slickspot Peppergrass By The Owyhee Harvester Ant, Joshua P. White

Boise State University Theses and Dissertations

1. (1) Seed predation can significantly restrict the reproductive output and individual fitness of plants, particular those plants that are rare or endangered. In some cases the total seed loss can reach 100%. Owyhee harvester ants, Pogonomyrmex salinus, actively remove the fruits and seeds of slickspot peppergrass, Lepidium papilliferum, a rare mustard endemic to southwest Idaho.
2. (2) Several experiments were conducted to quantify seed predation on L. papilliferum located within the foraging distance of P. salinus. Individuals exposed to harvester ants experienced a direct loss of fruits and seeds ( > 40%), whereas plants shielded from ants suffered almost …

New Species And Expanded Geographic Ranges Of Gut Fungi And Their Symbiotic Relationship With Insect Hosts, Molly Elizabeth Bench

Boise State University Theses and Dissertations

Trichomycetes from suitable immature aquatic lower dipteran, mayfly and stonefly hosts (Baetidae, Capniidae, Chironomidae, Nemouridae, and Simuliidae) were collected and identified biweekly over a twelve month period, from an ephemeral system, Cottonwood Creek, in Boise, Idaho. The abundances of eight species of obligate endosymbionts from the genera Genistelloides, Harpella, Lancisporomyces, Paramoebidium, Smittium, and Zygopolaris were evaluated with host abundance for potential correlative relationships. The abundances of all of the examined species of gut fungi, except Smittium elongatum and S. megazygosporum, were positively correlated with the abundances of the hosts. The two species with non-significant relationships with their hosts' abundance were …

Lead Bullet Fragments In Venison From Rifle-Killed Deer: Potential For Human Dietary Exposure, W. Grainger Hunt, Richard T. Watson, J. Lindsay Oaks, Chris N. Parish, Kurt K. Burnham, Russell L. Tucker, James R. Belthoff, Garret Hart

Biology Faculty Publications and Presentations

Human consumers of wildlife killed with lead ammunition may be exposed to health risks associated with lead ingestion. This hypothesis is based on published studies showing elevated blood lead concentrations in subsistence hunter populations, retention of ammunition residues in the tissues of hunter-killed animals, and systemic, cognitive, and behavioral disorders associated with human lead body burdens once considered safe. Our objective was to determine the incidence and bioavailability of lead bullet fragments in hunter-killed venison, a widely-eaten food among hunters and their families. We radiographed 30 eviscerated carcasses of White-tailed Deer (Odocoileus virginianus) shot by hunters with standard …

Correlation Between Animal And Mathematical Models For Prostate Cancer Progression, Zdzislaw Jackiewiczy, Cheryl L. Jorcyk, Mikhail K. Kolev, Barbara Zubik-Kowal

Biology Faculty Publications and Presentations

This work demonstrates that prostate tumour progression in vivo can be analysed by using solutions of a mathematical model supplemented by initial conditions chosen according to growth rates of cell lines in vitro. The mathematical model is investigated and solved numerically. Its numerical solutions are compared with experimental data from animal models. The numerical results confirm the experimental results with the growth rates in vivo.

Caspase Cleavage Of The Amyloid Precursor Protein Is Prevented After Overexpression Of Bcl-2 In A Triple Transgenic Mouse Model Of Alzheimer’S Disease, Debra K. Kumasaka, Veronica Galvan, Elizabeth Head, Troy T. Rohn

Biology Faculty Publications and Presentations

A recent study demonstrated the lack of beta-amyloid (Aβ) plaque formation and accumulation of the amyloid precursor protein (APP) in a triple transgenic mouse model of Alzheimer’s disease (3xTg-AD) following overexpression of the anti-apoptotic protein, Bcl-2 (Rohn et al., J. Neurosci. 28: 3051-9, 2008). The supposition from that study was the accumulation of APP resulted from a decrease in caspase-mediated processing of APP. To determine a direct role for the caspase-cleavage of APP in 3xTg-AD mice, we designed a site-directed caspasecleavage antibody to APP and demonstrated it is a specific marker for caspase-cleaved APP. Application of this antibody revealed neuronal …

Pathogenic Bacillus Anthracis In The Progressive Gene Losses And Gains In Adaptive Evolution, Gongxin Yu

Biology Faculty Publications and Presentations

Background: Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living to a strictly intracellular or host-depending life. It resulted in loss of function mutations and/or the acquisition of virulence gene clusters. Bacillus anthracis shares a common soil bacterial ancestor with its closely related bacillus species but is the only obligate, causative agent of inhalation anthrax within the genus Bacillus. The anthrax-causing Bacillus anthracis experienced the similar lifestyle changes. We thus hypothesized that the bacterial pathogen would follow a compatible evolution path. …

Caspase-Cleaved Tar Dna-Binding Protein-43 In Pick’S Disease, Troy T. Rohn, Polina Kokoulina

Biology Faculty Publications and Presentations

The hyperphosphorylation and proteolytic modification of the TAR DNA binding protein-43 (TDP-43) is a key finding in a number of neurodegenerative diseases including frontotemporal dementia with ubiquitin-positive inclusions (FTLD-U), amyotrophic lateral sclerosis (ALS), and most recently Alzheimer’s disease (AD). To examine whether proteolytic modifications of TDP-43 is a relevant finding in Pick’s disease, we utilized a novel site-directed caspase-cleavage antibody based upon a known caspase-3 cleavage consensus site within TDP-43 at position 219. Application of this antibody, termed TDP caspase-cleavage product (TDPccp) to postmortem Pick’s disease brain sections revealed the presence of caspase-cleaved TDP-43 in Pick and Hirano bodies predominantly …

An Exon-Based Comparative Variant Analysis Pipeline To Study The Scale And Role Of Frameshift And Nonsense Mutation In The Human-Chimpanzee Divergence, Gongxin Yu

Biology Faculty Publications and Presentations

Chimpanzees and humans are closely related but differ in many deadly human diseases and other characteristics in physiology, anatomy, and pathology. In spite of decades of extensive research, crucial questions about the molecular mechanisms behind the differences are yet to be understood. Here I report ExonVar, a novel computational pipeline for Exon-based human-chimpanzee comparative Variant analysis. The objective is to comparatively analyze mutations specifically those that caused the frameshift and nonsense mutations and to assess their scale and potential impacts on human-chimpanzee divergence. Genomewide analysis of human and chimpanzee exons with ExonVar identified a number of species-specific, …

Trichomycetes From Lentic And Lotic Aquatic Habitats In Ontario, Canada, D. B. Strongman, Merlin M. White

Biology Faculty Publications and Presentations

Fungi and protists make up an ecological group, trichomycetes, that inhabit the guts of invertebrates, mostly aquatic insects. Trichomycetes are reported herein from arthropods collected in lotic habitats (fast flowing streams) and lentic environments (ponds, ditches, seeps, and lakes) from 11 sites in Algonquin Park and 6 other sites in Ontario, Canada. Thirty-two trichomycete species were recovered, including 7 new species: Legeriomyces algonquinensis, Legeriosimilis leptocerci, Legeriosimilis whitneyi and Paramoebidium umbonatum are described from mayfly nymphs (Ephemeroptera); Pennella digitata and Glotzia incilis from black fly and midge larvae (Diptera), respectively; and Arundinula opeongoensis from a crayfish (Crustacea). Legeriomyces rarus Lichtw. & …

Ambient Temperature Influences Diet Selection And Physiology Of An Herbivorous Mammal, Neotoma Albigula, M. D. Dearing, Jennifer S. Forbey, J. D. Mclister, L. Santos

Biology Faculty Publications and Presentations

The whitethroat woodrat (Neotoma albigula) eats juniper (Juniperus monosperma), but the amount of juniper in its diet varies seasonally. We tested whether changes in juniper consumption are due to changes in ambient temperature and what the physiological consequences of consuming plant secondary compounds (PSCs) at different ambient temperatures might be. Woodrats were acclimated to either 20ºC or 28ºC. Later, they were given two diets to choose from (50% juniper and a nontoxic control) for 7 d. Food intake, resting metabolic rate (RMR), and body temperature (T_b) were measured over the last 2 d. Woodrats at 28ºC …

Caspase-Cleaved Tar Dna Binding Protein-43 Is A Major Pathological Finding In Alzheimer’S Disease, Troy T. Rohn

Biology Faculty Publications and Presentations

The TAR DNA binding protein-43 (TDP-43) has been identified as a major constituent of inclusions found in frontotemporal dementia with ubiquitin-positive inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS). To determine a possible role for TDP-43 in Alzheimer’s disease (AD), a site-directed caspase-cleavage antibody to TDP-43 based upon a known caspase-3 cleavage consensus site within TDP-43 at position D219 was designed. In vitro, this antibody labeled the predicted 25 kDa caspase-cleavage fragment of TDP-43 without labeling full-length TDP-43 following digestion of recombinant TDP-43 with caspase-3 or treatment of Hela cells with staurosporine. Application of this antibody in postmortem brain sections …

Intrafeather And Intraindividual Variation In The Stable-Hydrogen Isotope (Δd) Content Of Raptor Feathers, Adam D. Smith, Kara Donohue, Alfred M. Dufty Jr.

Biology Faculty Publications and Presentations

Stable-hydrogen isotope ratios (deuterium:protium; δD) in feathers enable researchers to evaluate patterns of avian movement and to estimate the source areas of migratory birds. However, variation in feather δD remains inadequately described, thus confounding inferences of avian movement and origin. We assessed variation within a feather and among feathers within and between tracts in three species of immature raptors. Within contour feathers, measurements of δD increased from a distal section to an adjacent, proximal section; the magnitude of δD increase varied with raptor species. Furthermore, contour and flight feathers differed systematically in their δD content. Two explanations for intrafeather and …