Digital Commons Network^™

Plant Neighbor Identity Influences Plant Biochemistry And Physiology Related To Defense, Amanda K. Broz, Corey D. Broeckling, Clelia De-La-Peña, Matthew R. Lewis, Erick Greene, Ragan M. Callaway, Lloyd W. Sumner, Jorge M. Vivanco

Biological Sciences Faculty Publications

Background: Chemical and biological processes dictate an individual organism's ability to recognize and respond to other organisms. A small but growing body of evidence suggests that plants may be capable of recognizing and responding to neighboring plants in a species specific fashion. Here we tested whether or not individuals of the invasive exotic weed, Centaurea maculosa, would modulate their defensive strategy in response to different plant neighbors. Results: In the greenhouse, C. maculosa individuals were paired with either conspecific (C. maculosa) or heterospecific (Festuca idahoensis) plant neighbors and elicited with the plant defense signaling molecule methyl jasmonate to mimic insect …

Infrageneric Relationships Within Collomia (Polemoniaceae), Eric Stewart Green

Theses and Dissertations

Traditional evolutionary models depict evolution as a bifurcating pattern with a single ancestor diverging to form two lineages. However, reticulate species resulting from hybridization and recombination have unique histories shared with two independent lineages, not one. Accounting for the genetic histories of reticulate species increases the power and ability to recover biologically meaningful relationships. The genus Collomia (Polemoniaceae) is used to explore issues of reticulation and the importance of accounting for gene histories in a phylogenetic analysis. The issue of reticulation within species trees is discussed with a multilabeled, network approach being explored to better represent the genus's evolutionary history. …

Identification Of Multiple Vasotocin Receptor Cdnas In Teleost Fish: Sequences, Phylogenetic Analysis, Sites Of Expression, And Regulation In The Hypothalamus And Gill In Response To Hyperosmotic Challenge, Sean C. Lema

Biological Sciences

Vasopressin and its homolog vasotocin regulate hydromineral balance, stress responses, and social behaviors in vertebrates. In mammals, the functions of vasopressin are mediated via three classes of membrane-bound receptors: V1a-type, V1b-type and V2-type. To date, however, only a single class of vasotocin receptor has been identified in teleost fish. Here, cDNAs encoding three putative vasotocin receptors – two distinct V1a-type receptor paralogs (V1a1 and V1a2) and a previously undescribed V2- type receptor (V2) – and a single isotocin receptor were isolated and sequenced from the Amargosa pupfish (Cyprinodon nevadensis amargosae). RT-PCR revealed that mRNAs …

Ocean Currents Help Explain Population Genetic Structure, Crow White, Kimberly A. Selkoe, James Watson, David A. Siegel, Danielle C. Zacherl, Robert J. Toonen

Biological Sciences

No abstract provided.

Candidate Genes For Chromosomes 6 And 10: Quantitative Trait Loci For Age-Related Retinal Degeneration In Mice, D.G. Ogando, Kam D. Dahlquist, M. Alizadeh, K. Kunchithapautham, J. Li, N. Yu, M.M. Lavail, B. Rohrer, D. Vollrath, M. Danciger

Biology Faculty Works

Purpose: In a previous study, several quantitative trait loci (QTL) that influence age-related degeneration (ageRD) were identified in a cross between the albino strains B6(Cg)-Tyr(c-2J)/J (B6a) and BALB/cByJ (C). The Chromosome (Chr) 6 and Chr 10 QTL were the strongest and most highly significant loci and both involved B6a protective alleles. The QTL were responsible for 21% and 9% of the variance in phenotypes, respectively. We focused on these two QTL to identify candidate genes. Methods: DNA microarrays were used for the two mouse strains at four and eight months of age to identify genes that are differentially regulated and …

Tooth Chipping Can Reveal The Diet And Bite Forces Of Fossil Hominins, Paul J. Constantino, James Jin-Wu Lee, Herzl Chai, Bernhard Zipfel, Charles Ziscovici, Brian R. Lawn, Peter W. Lucas

Biological Sciences Faculty Research

Mammalian tooth enamel is often chipped, providing clear evidence for localized contacts with large hard food objects. Here, we apply a simple fracture equation to estimate peak bite forces directly from chip size. Many fossil hominins exhibit antemortem chips on their posterior teeth, indicating their use of high bite forces. The inference that these species must have consumed large hard foods such as seeds is supported by the occurrence of similar chips among known modern-day seed predators such as orangutans and peccaries. The existence of tooth chip signatures also provides a way of identifying the consumption of rarely eaten foods …

Behavioural Display Systems Across Nine Anolis Lizard Species: Sexual Dimorphisms In Structure And Function, Michele A. Johnson, J. Wade

Biology Faculty Research

Relationships between structure and function are a primary focus in biology, yet they are most often considered within individual species. Sexually dimorphic communication behaviours and the morphology of associated structures can vary widely, even among closely related species, and these traits provide an ideal opportunity to investigate the evolution of structure-function patterns. Using nine Anolis lizard species, we addressed a series of questions regarding sex differences in and the evolution of relationships between extension of the throat fan (dewlap) and morphology of the muscles and cartilage controlling it. The main results indicated that within species, males displayed the dewlap more …

Body Size And Social Dominance Influence Breeding Dispersal In Male Pachydiplax Longipennis (Odonata), Shannon Mccauley

Biological Sciences

1. Dispersal behaviour can be affected by an individual's phenotype, by the environmental or social context they experience, and by interactions between these factors. Differential dispersal propensities between individuals may also be an important modifier of functional connectivity between populations. To assess how a key trait, body size, affected both social interactions and dispersal behaviour, this study examined the relationship between body size, antagonistic interactions, and breeding dispersal in male dragonflies (Pachydiplax longipennis) across a seasonal decline in adult body size. 2. During a seasonal peak in male body size in this study, dispersers were smaller than non-dispersers. Later in …

North American Montane Red Foxes: Expansion, Fragmentation, And The Origin Of The Sacramento Valley Red Fox, Benjamin N. Sacks, Mark J. Statham, John D. Perrine, Samantha M. Wisely, Keith B. Aubry

Biological Sciences

Most native red foxes (Vulpes vulpes) in the western contiguous United States appear to be climatically restricted to colder regions in the major mountain ranges and, in some areas, have suffered precipitous declines in abundance that may be linked to warming trends. However, another population of unknown origin has occurred in arid habitats in the Sacramento Valley of California well outside this narrow bioclimatic niche since at least 1880. If native, this population would be ecologically distinct among indigenous North American red foxes. We used mitochondrial and microsatellite markers from historical and modern samples (modes: 1910–1930 and 2000–2008, …

The Evolution Of Seeds, Ada Linkies, Kai Graeber, Charles A. Knight, Gerhard Leubner-Metzger

Biological Sciences

The evolution of the seed represents a remarkable life-history transition for photosynthetic organisms. Here, we review the recent literature and historical understanding of how and why seeds evolved. Answering the 'how' question involves a detailed understanding of the developmental morphology and anatomy of seeds, as well as the genetic programs that determine seed size. We complement this with a special emphasis on the evolution of dormancy, the characteristic of seeds that allows for long 'distance' time travel. Answering the 'why' question involves proposed hypotheses of how natural selection has operated to favor the seed life-history phenomenon. The recent flurry of …

Design And Implementation Of Marine Biology Lessons At The Avila Beach Sea Life Center, Heather L. Price

Biological Sciences

No abstract provided.

The Anorexigenic And Hypertensive Effects Of Nesfatin-1 Are Reversed By Pretreatment With An Oxytocin Receptor Antagonist, Gina L.C. Yosten, Willis K. Samson

Biological Sciences Faculty Research & Creative Works

Nesfatin-1 is an 82-amino acid protein encoded by the nucleobindin2 gene. When injected intracerebroventricularly, nesfatin-1, via a melanocortin 3/4 receptor-dependent mechanism, potently decreased both food and water intakes and elevated mean arterial pressure in a dose-related manner. Because nesfatin-1 colocalized with oxytocin in hypothalamus and because nesfatin-1 had direct depolarizing effects on oxytocin-producing neurons in hypothalamic slice preparations, we hypothesized that the actions of nesfatin-1 required the presence of functional oxytocin receptors. We, therefore, pretreated conscious, unrestrained male rats with the oxytocin receptor antagonist, ornithine vasotocin (OVT), before treatment with nesfatin-1. We found that pretreatment with OVT reversed the effects …

Future Management Of The Metropolitan Recreational Roe's Abalone Fishery., Metropolitan Roe's Abalone Recreational Fishery Working Group.

Fisheries Management Papers

Following the setting of a 40 tonne Total Allowable Recreational Catch (TARC) for the Perth recreational abalone fishery, a working group was formed to examine future management options.

The Metropolitan Roe’s Abalone Recreational Fishery Working Group (“the Working Group”) examined historical management, key principles, amenity of fishing, bag limits, license numbers, season length and timing of the season to assist its deliberations. A questionnaire was also sent out to 1,000 abalone recreational licence holders, with 20 per cent of licensees providing a detailed response.

Alpha-Synuclein Delays Endoplasmic Reticulum (Er)-To-Golgi Transport In Mammalian Cells By Antagonizing Er/Golgi Snares, Nandhakumar Thayanidhi, Jared R. Helm, Deborah C. Nycz, Marbin Bentley, Yingjian Liang, Jesse C. Hay

Biological Sciences Faculty Publications

Toxicity of human alpha-synuclein when expressed in simple organisms can be suppressed by overexpression of endoplasmic reticulum (ER)-to-Golgi transport machinery, suggesting that inhibition of constitutive secretion represents a fundamental cause of the toxicity. Whether similar inhibition in mammals represents a cause of familial Parkinson's disease has not been established. We tested elements of this hypothesis by expressing human alpha-synuclein in mammalian kidney and neuroendocrine cells and assessing ER-to-Golgi transport. Overexpression of wild type or the familial disease-associated A53T mutant alpha-synuclein delayed transport by up to 50%; however, A53T inhibited more potently. The secretory delay occurred at low expression levels and …

Antibiotic Administration Alters The Community Structure Of The Gastrointestinal Micobiota, Courtney Robinson, Vincent Young

Department of Biology Faculty Publications

We recently demonstrated that antibiotic administration has a reproducible effect on the community structure of the indigenous gastrointestinal microbiota of mice. In this addendum we report on additional experimentation using the antibiotic vancomycin. In accord with our previous findings, vancomycin administration results in consistent alteration of the microbiota of the cecal contents and the cecal mucosa. These alterations are largely reversed by a three-week period of recovery without antibiotics. In contrast to our previous results using other antibiotics, the alterations in community structure associated with vancomycin occured without a significant decrease in the overall bacterial biomass. These results indicate that …

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. …

Recent Advances In The Climate Change Biology Literature: Describing The Whole Elephant, A. Townsend Peterson, Shaily Menon, Xingong Li

Peer Reviewed Publications

Climate change biology is seeing a wave of new contributions, which are reviewed herein. Contributions treat shifts in phenology and distribution, and both document past and forecast future effects. However, many of the current wave of contributions are observational and correlational, and few are experimental in nature, and too often a conceptual framework in which to contextualize the results is lacking. An additional gap is the lack of effective cross-linking among areas of research, for example, connection of sea-level rise and climate change implications for distributions of species, or evolutionary adaptation studies with distributional shift studies. Although numerous important contributions …

Endocannabinoid Signalling: Has It Got Rhythm?, Linda K. Vaughn, Gerene Denning, Kara L. Stuhr, Harriet De Wit, Matthew N. Hill, Cecilia J. Hillard

Biomedical Sciences Faculty Research and Publications

Endogenous cannabinoid signalling is widespread throughout the body, and considerable evidence supports its modulatory role in many fundamental physiological processes. The daily and seasonal cycles of the relationship of the earth and sun profoundly affect the terrestrial environment. Terrestrial species have adapted to these cycles in many ways, most well studied are circadian rhythms and hibernation. The purpose of this review was to examine literature support for three hypotheses: (i) endocannabinoid signalling exhibits brain region-specific circadian rhythms; (ii) endocannabinoid signalling modulates the rhythm of circadian processes in mammals; and (iii) changes in endocannabinoid signalling contribute to the state of hibernation. …

Chemical Inhibition Of Caax Protease Activity Disrupts Yeast Ras Localization, Surya P. Mandahar, Emily R. Hildebrandt, William H. Jacobsen, George M. Santangelo, Walter K. Schmidt

Faculty Publications

Proteins possessing a C-terminal CaaX motif, such as the Ras GTPases, undergo extensive post-translational modification that includes attachment of an isoprenoid lipid, proteolytic processing and carboxylmethylation. Inhibition of the enzymes involved in these processes is considered a cancer-therapeutic strategy. We previously identified nine in vitro inhibitors of the yeast CaaX protease Rce1p in a chemical library screen (Manandhar et al., 2007). Here, we demonstrate that these agents disrupt the normal plasma membrane distribution of yeast GFP-Ras reporters in a manner that pharmacologically phenocopies effects observed upon genetic loss of CaaX protease function. Consistent with Rce1p being the in vivo target …

Evaluating Captive-Breeding Techniques And Reintroduction Success Of The California Condor (Gymnogyps Californianus), Amy C. Utt

Loma Linda University Electronic Theses, Dissertations & Projects

In this dissertation, I present two original research studies on the behavior and survival of the critically endangered California Condor (Gymnogyps californianus). I also provide a comprehensive review of the role of captive-rearing to the conservation of birds.

The first study examined the behavioral differences of puppet- and parent-reared condor juveniles reared in captivity. This study further defined and examined the behaviors of adult conspecific mentors and their interactions with juveniles. Dominance hierarchy analyses for two cohorts of juveniles and their adult mentors indicated the establishment of a linear hierarchy. Although puppet-reared juveniles engaged in fewer social behaviors in …

A Sea Change For Aquatic Sustainability : Meeting The Challenge Of Fish Resources Management And Aquatic Sustainability In The 21st Century, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Diversity Of Oligotrichia And Choreotrichia Ciliates In Coastal Marine Sediments And In Overlying Plankton, Mary Doherty, Maiko Tamura, Jan A.C. Vriezen, George B. Mcmanus, Laura A. Katz

Biological Sciences: Faculty Publications

Elucidating the relationship between ciliate communities in the benthos and the plankton is critical to understanding ciliate diversity in marine systems. Although data for many lineages are sparse, at least some members of the dominant marine ciliate clades Oligotrichia and Choreotrichia can be found in both plankton and benthos, in the latter either as cysts or active forms. In this study, we developed a molecular approach to address the relationship between the diversity of ciliates in the plankton and those of the underlying benthos in the same locations. Samples from plankton and sediments were compared across three sites along the …

Bioaugmentation For Improved Recovery Of Anaerobic Digesters After Toxicant Exposure, Anne Schauer-Gimenez, Daniel Zitomer, James Maki, Craig Struble

Biological Sciences Faculty Research and Publications

Bioaugmentation was investigated as a method to decrease the recovery period of anaerobic digesters exposed to a transient toxic event. Two sets of laboratory-scale digesters (SRT = 10 days, OLR = 2 g COD/L-day), started with inoculum from a digester stabilizing synthetic municipal wastewater solids (MW) and synthetic industrial wastewater (WW), respectively, were transiently exposed to the model toxicant, oxygen. Bioaugmented digesters received 1.2 g VSS/L-day of an H₂-utilizing culture for which the archaeal community was analyzed. Soon after oxygen exposure, the bioaugmented digesters produced 25–60% more methane than non-bioaugmented controls (p < 0.05). One set of digesters produced lingering high propionate concentrations, and bioaugmentation resulted in significantly shorter recovery periods. The second set of digesters did not display lingering propionate, and bioaugmented digesters recovered at the same time as non-bioaugmented controls. The difference in the effect of bioaugmentation on recovery may be due to differences between microbial communities of the digester inocula originally employed. In conclusion, bioaugmentation with an H₂-utilizing culture is a …

Behavior And Physiology Of Hermit Crabs During Burial: Shell Abandonment And Lactate Accumulation, Janelle Allison Shives

Loma Linda University Electronic Theses, Dissertations & Projects

Organisms living in the intertidal zone must adapt to environmental and physical stressors. One physical stressor that these organisms may face, and that may require specific behavioral and physiological responses, is burial by sediment. In this thesis I report the results of experiments in which I subjected the intertidal hermit crab, Pagurus samuelis, to burial and analyzed aspects of subsequent behavior and physiology. In the first set of experiments, hermit crabs were buried with the shell aperture facing either up or down, and at one of three depths (2, 4, or 6 cm). The factors hermit crab weight, shell …

Chk2 Is Negatively Regulated By Protein Phosphatase 2a, Alyson Freeman

USF Tampa Graduate Theses and Dissertations

Checkpoint kinase 2 (CHK2) is an effector kinase of the DNA damage response pathway and although its mechanism of activation has been well studied, the attenuation of its activity following DNA damage has not been explored. Here, we identify the B'α subunit of protein phosphatase 2A (PP2A), a major protein serine/threonine phosphatase of the cell, as a CHK2 binding partner and show that their interaction is modulated by DNA damage. B'α binds to the SQ/TQ cluster domain of CHK2, which is a target of ATM phosphorylation. CHK2 is able to bind to many B' subunits as well as the PP2A …

Investigation Of Science Education Attitudes In Alternative High School Settings, Sarah Jane Rogers

Theses and Dissertations

This study compared the attitudes of administrators, teachers and students in school settings for at-risk students. Students are considered at-risk if they are not academically successful. Teacher and student science education attitudes were analyzed by survey data and categorization of teaching practices. Additionally, data from classroom videotapes and teacher interviews was collected to support and triangulate survey data. Study participants were selected from two school settings for at-risk students 1) public alternative schools (PAS) and 2) private residential treatment centers (RTC). When the survey questions were analyzed by school type and teacher classification several differences were found between 1) teacher …

Documenting Lineages From My ‘Littlest Ancestor’ To My Deep Ancestral Roots, Emily F. Schmitt Lavin

Biology Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Platform Effects On Optical Variability And Prediction Of Underwater Visibility, Grace Chang, Michael S. Twardowski, Yu You, Mark A. Moline, Peng-Wang Zhai, Scott Freeman, Matthew Slivkoff, Francesco Nencioli, George W. Kattawar

Biological Sciences

We present hydrographic and optical data collected concurrently from two different platforms, the R/P FLoating Instrument Platform and the R/V Kilo Moana, located about 2km apart in the Santa Barbara Channel in California. We show that optical variability between the two platforms was due primarily to platform effects, specifically the breakdown of stratification from mixing by the hull of R/P FLIP. Modeled underwater radiance distribution differed by as much as 50% between the two platforms during stratified conditions. We determine that the observed optical variability resulted in up to 57% differences in predicted horizontal visibility of a black target.

Genomic Organization And Molecular Phylogenies Of The Beta (Β) Keratin Multigene Family In The Chicken (Gallus Gallus) And Zebra Finch (Taeniopygia Guttata): Implications For Feather Evolution, Matthew J. Greenwold, Roger H. Sawyer

Faculty Publications

Background: The epidermal appendages of reptiles and birds are constructed of beta (β) keratins. The molecularphylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes ofthe chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β- keratins,but to study their molecular evolution in archosaurians.

Results: The subfamilies (claw, feather, feather-like, and scale) of β-keratin genes are clustered in the same 5' to 3' orderon microchromosome 25 in chicken and zebra finch, …

Microbial Stoichiometry And Homeostasis Of Nutrient Ratios In Fungi, Desiree Leach

Honors Theses

Stoichiometry is the ratio of elements in a substance or microbial biomass. This paper investigates microbial stoichiometry and the responses of microbes to dissolved nutrient concentrations and ratios. The current work assesses both autrotrophic and heterotrophic responses to nutrient enrichment: autotrophic and heterotrophic states are defined mainly by ecosystem primary production and respiration. In ecosystems dominated by autotrophic microbes, nutrient enrichment can lead to increased biomass and biomass-specific rates of primary production. Heterotrophic ecosystems rely on subsides of organic carbon from outside the system. Their enrichment with N and/or P can accelerate microbial respiration rates and result in carbon losses …