Integrative Biology Commons^™

Bacterial Colonization And Extinction On Marine Aggregates: Stochastic Model Of Species Presence And Abundance, Andrew M. Kramer, M. Maille Lyons, Fred C. Dobbs, John M. Drake

Integrative Biology Faculty and Staff Publications

Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while …

Mitochondrial Dna Assessment Of The Phylogeography Of The Gopher Tortoise, Joshua R. Ennen, Brian R. Kreiser, Carl P. Qualls, Daniel Gaillard, Matthew Aresco, Roger Birkhead, Tracey Tuberville, Earl D. Mccoy, Henry R. Mushinsky, Thomas W. "Bill" Hentges, Aaron W. Schrey

Integrative Biology Faculty and Staff Publications

Identifying geographic barriers that define genetic structure within a species is crucial in formulating an effective conservation plan. The identification of appropriate management units is critical for the protection and recovery of the gopher tortoise Gopherus polyphemus, which have declined across their entire range. Previous molecular work at various spatial scales has identified distinct population assemblages of the gopher tortoise. The goal of this study was to assess the genetic structure in gopher tortoises through a more complete sampling of the federally listed as threatened portion of the range and evaluate the extent of genetic isolation imposed by several …

A Plant Virus Substrate Induces Early Upregulation Of Bmp2 For Rapid Bone Formation, Pongkwan Sitasuwan, L. Andrew Lee, Peng Bo, Erin N. Davis, Yuan Lin, Qian Wang

Faculty Publications

Many nanoscale materials have been developed to investigate the effects on stem cell differentiations via topographical and chemical cues for applications in tissue engineering and regenerative medicine. The use of plant viruses as cell supporting substrates has been of particular interest due to the rapid induction of bone marrow derived mesenchymal stem cells (BMSCs) towards osteogenic cells. In this study, the role of Tobacco mosaic virus (TMV) and its early effects on osteoinduction with particular emphasis on the regulation of bone morphogenetic protein-2 (BMP2) was examined. We observed that the cells on the virus substrate immediately aggregated and formed bone-like …

Phylogenetic Search Through Partial Tree Mixing., Kenneth Sundberg, Mark Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith Crandall

Computational Biology Institute

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda

CONCLUSIONS: The use of Partial Tree Mixing …

Testing Phylogenetic Hypotheses Of The Subgenera Of The Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)., Jesse W Breinholt, Megan L Porter, Keith A Crandall

Computational Biology Institute

BACKGROUND: The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.

METHODOLOGY/PRINCIPAL FINDINGS: We use three mitochondrial and one nuclear gene …

Salinity Preference Of Alaskan Threespine Stickleback: Test For Divergence In Halotaxis Between Ancestral And Landlocked Populations, David Fryxell, Eric T. Schultz

EEB Articles

Glacial retreat during the Pleistocene caused landlocking of anadromous Alaskan threespine stickleback, Gasterosteus aculeatus, furnishing a natural ‘experiment’ in osmoregulatory divergence. The objective of this study was to assess the effects of individual acclimation and population divergence on salinity preference. Full-sibling families of marine, anadromous, and freshwater-landlocked populations of stickleback were reared in common environments until 3 weeks post-hatch, then were split and acclimated to low or high salinity. At 6 to 8 weeks of age the six experimental groups were tested for salinity preference in a tank that offers fish a choice of compartments with different salinities arranged …

Ramphotyphlops Braminus (Brahminy Blindsnake): Predation, Louis A. Somma

Papers in Herpetology

Ramphotyphlops braminus currently has the most widespread, near worldwide, nonindigenous distribution of any snake. In Florida, USA, R. braminus is rapidly expanding its distribution.

The stomach contents of a necropsied Dasypus novemcinctus (nine-banded armadillo) found on the premises of the Florida Department of Agriculture and Consumer Services in Gaisesville in March 2011 included an intact adult R. braminus. Dasypus novemcinctus is nonindigenous in Florida. It has a primarily insectivorous diet but occasionally preys upon small vertebrates, including reptiles. This is the first record of R. braminus in the diet of D. novemcinctus.

Demasculinization And Feminization Of Male Gonads By Atrazine: Consistent Effects Across Vertebrate Classes, Krista A. Mccoy

Integrative Biology Faculty and Staff Publications

Atrazine is the most commonly detected pesticide contaminant of ground water, surface water, and precipitation. Atrazine is also an endocrine disruptor that, among other effects, alters male reproductive tissues when animals are exposed during development. Here, we apply the nine so-called “Hill criteria” (Strength, Consistency, Specificity, Temporality, Biological Gradient, Plausibility, Coherence, Experiment, and Analogy) for establishing cause–effect relationships to examine the evidence for atrazine as an endocrine disruptor that demasculinizes and feminizes the gonads of male vertebrates. We present experimental evidence that the effects of atrazine on male development are consistent across all vertebrate classes examined and we present a …

Role Of Porcine Reproductive And Respiratory Syndrome Virus Non-Structural Protein 1 In Viral Replications And Pathogenesis, Lalit Kumar Beura

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

Porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious agent of significant concern to the global swine industry. PRRSV infection of pigs is initiated by a long viremia after which the virus enters in an extended persistent phase of 3-4 months that ultimately is resolved by the immune system. The delayed and weak host adaptive response is responsible for the protracted convalescence period. An initial sub-optimal innate immune response is postulated to be the reason behind such meager adaptive immune response. A major focus of the studies undertaken in this dissertation was to identify the viral non-structural proteins (nsps) …

Relative Abundance Of Mitochondria Rich Cell Types In Threespine Stickleback: Interpopulation Differences And Salinity Effects, Dante Paolino

Honors Scholar Theses

The objective of this study is to determine whether there are evolutionary trade-offs among populations isolated to different salinities in nature with regards to mitochondria rich (MR) cell production. We expected differences among populations in MR cell abundances due to the energy requirements needed to maintain and produce these cells. Eggs from three populations of threespine stickleback (Gasterosteus aculeatus) were hatched and reared for 10 weeks and then the fish were put into one of two salinity challenges: either 0.4 ppt freshwater or 35 ppt saltwater for 13 days. The populations consisted of one isolated to freshwater, one isolated …

Blood-Brain Barrier Impairment In An Animal Model Of Mps Iii B, Svitlana N. Garbuzova-Davis, Michael Louis, Edward M. Haller, Hiranya M. Derasari, Ashley E. Rawls, Paul R. Sanberg

Integrative Biology Faculty and Staff Publications

Background: Sanfilippo syndrome type B (MPS III B) is caused by a deficiency of α-N-acetylglucosaminidase enzyme, leading to accumulation of heparan sulfate within lysosomes and eventual progressive cerebral and systemic multiple organ abnormalities. However, little is known about the competence of the blood-brain barrier (BBB) in MPS III B. BBB dysfunction in this devastating disorder could contribute to neuropathological disease manifestations.

Methodology/Principal Findings: In the present study, we investigated structural (electron microscope) and functional (vascular leakage) integrity of the BBB in a mouse model of MPS III B at different stages of disease, focusing on brain structures known to experience …

From Energy Gradient And Natural Selection To Biodiversity And Stability Of Ecosystems, Bo Deng

Department of Mathematics: Faculty Publications

The purpose of this paper is to incorporate well-established ecological principles into a foodweb model consisting of four trophic levels --- abiotic resources, plants, herbivores, and carnivores. The underlining principles include Kimura's neutral theory of genetic evolution, Liebig's Law of the Minimum for plant growth, Holling's functionals for herbivore foraging and carnivore predation, the One-Life Rule for all organisms, and Lotka-Volterra's model for intraand interspecific competitions. Numerical simulations of the model led to the following statistical findings: (a) particular foodwebs can give contradicting observations on biodiversity and productivity, in particular, all known functional forms -- - positive, negative, sigmoidal, and …

Diversity Of Boletaceae In Peninsular Malaysia., Chan Hong Twu

Student Works (2010-2019)

The Boletaceae (Basidiomycetes) s.l. is a large family of putrescent mushrooms with pores. Members of this well-recognized family form one of the largest, critical fungal components of obligate, symbiotic mycorrhizal communities throughout the temperate and tropical forest ecosystems of the world. They are intimately involved with basic ecosystem processes such as nutrient cycling, nutrient uptake, and decomposition of organic matter. Favourable temperature and humidity conditions in Asian tropical forest support a wide diversity of boletes. However, the seasonality of fruiting, short-lived and often solitary fruiting bodies are major problems encountered when documenting their diversity in tropical forests. The diversity of …

Arbuscular Mycorrhizal Fungi: Factors Affecting Soil Organic Matter Storage, Carl Lee Rosier

Graduate Student Theses, Dissertations, & Professional Papers

Arbuscular mycorrhizal fungi (AMF) are soil fungi forming symbiotic associations with majority of land plants. AMF alter soil organic matter (SOM) directly through stabilization of soil aggregates and indirectly providing a path in which plant fixed C02 is transferred below-ground. Understanding contributions of AMF to SOM via protein production and stabilization of soil aggregates will greatly aid our understanding of soil carbon sequestration, nutrient cycling and mitigation of soil erosion. The work presented in chapter 2 challenges the glomalin extraction process and assesses the accuracy of the Bradford and monoclonal-antibody ELISA detection methods. My results clarify the contribution of glomalin …

Sexual Selection And Alternative Reproductive Tactics In Cyprinodon Elegans, Jennifer M. Gumm

Faculty Publications

In systems with alternative reproductive tactics (ARTs), males have discrete behaviors and morphologies that allow them to optimize their reproductive success in relation to others in the population. Males with different phenotypes directly compete with one another for mates, providing unique opportunities for studying social interactions within a species. Using the Comanche Springs pupfish, Cyprinodonelegans, a species with three alternative reproductive tactics, I examine how male behaviors and social interactions influence the reproductive success of each tactic.

Previous studies suggest that large territorial males have high reproductive success, while satellite males and female mimics must intrude into territories in order …

Swimming Dynamics And Propulsive Efficiency Of Squids Throughout Ontogeny, Ian K. Bartol, Paul S. Krueger, Joseph T. Thompson, William J. Stewart

Biological Sciences Faculty Publications

Synopsis Squids encounter vastly different flow regimes throughout ontogeny as they undergo critical morphological changes to their two locomotive systems: the fins and jet. Squid hatchlings (paralarvae) operate at low and intermediate Reynolds numbers (Re) and typically have rounded bodies, small fins, and relatively large funnel apertures whereas juveniles and adults operate at higher Re and generally have more streamlined bodies, larger fins, and relatively small funnel apertures. These morphological changes and varying flow conditions affect swimming performance in squids. To determine how swimming dynamics and propulsive efficiency change throughout ontogeny, digital particle image velocimetry (DPIV) and kinematic …

Evidence Of Compromised Blood-Spinal Cord Barrier In Early And Late Symptomatic Sod1 Mice Modeling Als, Svitlana N. Garbuzova-Davis, Samuel Saporta, Edward M. Haller, Irina Kolomey, Steven P. Bennett, Huntington Potter, Paul R. Sanberg

Integrative Biology Faculty and Staff Publications

Background: The blood-brain barrier (BBB), blood-spinal cord barrier (BSCB), and blood-cerebrospinal fluid barrier (BCSFB) control cerebral/spinal cord homeostasis by selective transport of molecules and cells from the systemic compartment. In the spinal cord and brain of both ALS patients and animal models, infiltration of T-cell lymphocytes, monocyte-derived macrophages and dendritic cells, and IgG deposits have been observed that may have a critical role in motor neuron damage. Additionally, increased levels of albumin and IgG have been found in the cerebrospinal fluid in ALS patients. These findings suggest altered barrier permeability in ALS. Recently, we showed disruption of the BBB and …

The Origin Of 2 Sexes Through Optimization Of Recombination Entropy Against Time And Energy, Bo Deng

Department of Mathematics: Faculty Publications

Sexual reproduction in nature requires two sexes, which raises the question why the reproductive scheme did not evolve to have three or more sexes. Here we construct a constrained optimization model based on the communication theory to analyze trade-offs among reproductive schemes with arbitrary number of sexes. More sexes on one hand lead to higher reproductive diversity, but on the other hand incur greater cost in time and energy for reproductive success. Our model shows that the two-sexes reproduction scheme maximizes the recombination entropy-to-cost ratio, and hence is the optimal solution to the problem.

Why Is The Number Of Dna Bases 4?, Bo Deng

Department of Mathematics: Faculty Publications

In this paper we construct a mathematical model for DNA replication based on Shannon’s mathematical theory for communication. We treatDNAreplication as a communication channel. We show that the mean replication rate is maximal with four nucleotide bases under the primary assumption that the pairing time of the G–C bases is between 1.65 and 3 times the pairing time of the A–T bases.

Immune-Endocrine Interactions In The Lizard Sceloporus Undulatus Hyacinthinus: Testing An Assumption Of The Immunocompetence Handicap Hypothesis, Mukta Chakraborty

All-Inclusive List of Electronic Theses and Dissertations

The immunocompetence handicap hypothesis (IHH) was proposed by Folstad and Karter ( 1992) to describe the role of the endocrine system in ensuring honesty of sexual signaling. Numerous studies have investigated the assumptions of the IHH, but currently there is mixed evidential support in favor of the IHH. The first chapter of this thesis is a review examinining these studies, their limitations, and proposed alternative models and future directions. The second chapter of this thesis presents a study in which we experimentally assesss the testosterone immunosuppression assumption in adult male Sceloporus undulatus lizards. We manipulated circulating androgen levels (Day 0) …

Assessment Of Biogeochemical Deposits In Landfill Drainage Systems, Audrey D. Levine, Valerie J. Harwood, Antonio J. Cardoso, Lisa R. Rhea, Bina S. Nayak, Barbara M. Dodge, Mindy L. Decker, George Dzama, Lawrence Jones, Edward Haller

Integrative Biology Faculty and Staff Publications

Design, operation, and closure practices for Class I municipal solid waste (MSW) landfills are based on RCRA Subtitle D requirements for control of leachates and gases generated during the life of the landfill. Because leachate is generated as a result of water percolating through the landfill and waste consolidation, it contains dissolved and suspended materials that reflect the characteristics of the material it contacts. Over the past two decades significant changes have occurred in the characteristics of the waste streams that are disposed in landfills. In addition, many Florida municipalities have implemented Waste-to-Energy (WTE) systems. The WTE ash is either …

Agribusiness Sheep Updates - 2004 Part 3, Ken Hart, Keith Croker, Rob Davidson, Mario D'Antuono, Evan Burt, Tanya Kilminster, Diana Fedorenko, Darryl Mcclements, Robert Beard, Sandy Turton, Martin Atwell, Robert Beard

Sheep Updates

Posters Can Merino Ewes be Teased to Synchronise Oestrus for a Summer/Autumn Mating? Ken Hart, Keith Croker, Department of Agriculture Western Australia, Rob Davidson, School of Animal Biology, University of Western Australia. Mario D'Antuono, Department of Agriculture Western Australia Damara Sheep: Now Looking Domestic Evan Burt and Tanya Kilminster, Department of Agriculture Western Australia Production and Water Use of Lucerne and French Serradella Under Three Sowing Rates Diana Fedorenko1,4, Darryl McClements1,4 , Robert Beard3,4 1Department of Agriculture, 3 Farmer, Meckering, 4CRC for Plant-based Management of Dryland Salinity. E-SHEEP - Individual Animal Management is here Sandy Turton & Martin Atwell, Department …

Re-Assessment Of Carrying Capacities In The Ashburton River Catchment, Alan L. Payne, A M E Van Vreeswyk, K A. Leighton

Agriculture reports

Potential carrying capacities for land systems in the catchment of the Ashburton River were first estimated in 1983 as a result of a rangeland survey of the area undertaken during 1976, 1977 and 1978. Potential carrying capacity (termed capability capacity in the 1988 report) is a suggested sustainable level of use assuming that all pastures are in good range condition, the entire station is adequately watered for the effective management of livestock and seasonal conditions are average.

The Ashburton Land Conservation District Committee had previously requested a re-assessment of carrying capacities for Ashburton stations following the widespread establishment of buffel …

In Situ Of Interferon On Human Glioma Protein Kinase C-Α And -Β Ultrastructural Localization, Mildred Acevedo-Duncan, John Collins, Ruonana Zhang, Edward M. Haller, Charles E. Chalfant, Denise R. Cooper

Integrative Biology Faculty and Staff Publications

Transmission electron microscopy was used to determine how immunogold labeling of PKC-alpha or -beta is modulated by the antitumor drug IFN (HuIFN alpha-2b) in the cytoplasm, membrane structures, and nucleus of rapidly dividing and confluent human glioma U-373 cells. Results showed that except for nuclear localization, there were no specific cytoplasmic organelles that PKC-alpha or -beta translocated to following HuIFN alpha-2b treatment. Electron micrographs of PKC-beta in proliferating cells depicted 1.34-fold more PKC-beta in the nucleus than in the cytoplasm and a 1-min HuIFN alpha-2b (500 units/ml) treatment transiently increased PKC-beta immunoreactivity in the cytoplasm (1.95-fold) and nucleus (1.97-fold). In …

Effects Of Moose Foraging On Browse Availability In New Hampshire Deer Yards, Michael T. Pruss, Peter J. Pekins

New Hampshire Agricultural Experiment Station Publications

Food habits of moose (Alces alces) and white-tailed deer (Odocoileus virginianus) overlap in northern New Hampshire during autumn and winter. High moose and deer densities in deer yards, where deer may be confined for extended periods, could result in competition for limited deciduous forage. The purpose of this study was to investigate possible impacts by moose on browse availability in deer yards, and the potential effects on deer. Fifteen deer yards were studied in northern New Hampshire during spring and fall, 1990-91. Unbrowsed and browsed deciduous twigs, and deer and moose pellet groups were counted on 900 permanent plots to …

The Water Vapor Conductance Of Squamate Reptilian Eggs: The Influence Of Scaling On Nesting Ecology., Louis A. Somma

Papers in Herpetology

Flexible-shelled eggs of squamate reptiles are strongly influenced by their surrounding microclimate, particularly the hydric conditions of the nest. The eggshell water vapor conductance of an egg can be an indication of its requirement for water from the nest. Ackerman et al. (1985. Physiol. Zool. 58:129-137) have described the scaling relationship for eggshell water vapor conductance (G_H2O) of flexible-shelled reptilian eggs (G_H2O = 981.8M^0.52). This scaling relationship was investigated with water vapor conductance data obtained from 8 species of lizards representing the families Iguanidae (Anolis carolinensis, A. sagrai, Sceloporus woodi, S. virgatus) …

Elaphe Bairdi (Baird’S Rat Snake): Drinking Behavior., Louis A. Somma

Papers in Herpetology

On 13 February 1988. at 1600 h. a captive-bred (hatched July 1985) male Elaphe bairdi (TL.136.9 cm, SVL .. 89.54 cm). maintained in a 50.5 x 25 x 30 cm terrerium was accidently splashed with water. As beads of water on the snake's head rolled down to the upper labial sceles. swallowing was observed. The water on the labial scales was drawn Into the mouth while It was closed. This behavior lasted 42 sec. This behavior was repeated 23 out of 24 trials conducted during the next 24 days. The duration of swallowing wes 9-62 sec (avg 35.8, N = …

What Controls Tropical Reef Fish Populations: Recruitment Or Benthic Mortality? An Example In The Caribbean Reef Fish Haemulon Flavolineatum, M. J. Shulman, John C. Ogden

Integrative Biology Faculty and Staff Publications

Recruitment from a planktonic larval stage has been proposed to be an important factor in limiting populations of marine organisms, particularly tropical reef fishes. We monitored recruitment and population densities of juvenile size classes In French grunt Haemulon flavolineatum (Haemulidae) from October 1978 through December 1980 In a portion of Tague Bay, St. Croix, U. S. Virgin Islands. Within our study area, 95 % of new recruits settled onto the sand and seagrass lagoon floor and within a few weeks migrated to nearby reefs; the remaining 5'10 settled directly onto reef structures. Mean annual recruitment rate was 1.8 recruits per …

Recruitment Patterns In Young French Grunts, Haemulon Flavolineatum (Family Haemulidae), At St. Croix, Virgin Islands., William N. Mcfarland, E. B. Brothers, John C. Ogden, Myra J. Shulman, E. L. Bermingham, N. M. Kotachian-Prentiss

Integrative Biology Faculty and Staff Publications

No abstract provided.

Herbivory Effects On Thalassia Testudinum Leaf Growth And Nitrogen Content, J. C. Zieman, R. L. Iverson, John C. Ogden

Integrative Biology Faculty and Staff Publications

The pattern of turtle grazing on Thalassia testudinum in St. Croix seagrass beds begins with the establishment of a grazing plot by initial removal of leaf blades, followed by repeated grazing of several centimeter-long leaf blades within a maintained grazing area. Plants within the grazed area exhibit increased specific growth rate as a consequence of increased light flux to unepiphytized leaf bases. Leaf width is reduced in the grazed area as a consequence of grazing stress. The leaf bases contain a higher proportion of nitrogen and a lower lignin content than the leaf tips, in addition to lacking epiphytes. Our …