Digital Commons Network^™

Chemical Modification Of Reactive Multilayered Films Fabricated From Poly(2-Alkenyl Azlactone)S: Design Of Surfaces That Prevent Or Promote Mammalian Cell Adhesion And Bacterial Biofilm Growth, Maren E. Buck, Anthony S. Breitbach, Sonja K. Belgrade, Helen E. Blackwell, David M. Lynn

Chemistry: Faculty Publications

We report an approach to the design of reactive polymer films that can be functionalized post-fabrication to either prevent or promote the attachment and growth of cells. Our approach is based on the reactive layer-bylayer assembly of covalently crosslinked thin films using a synthetic polyamine and a polymer containing reactive azlactone functionality. Our results demonstrate (i) that the residual azlactone functionality in these films can be exploited to immobilize amine-functionalized chemical motifs similar to those that promote or prevent cell and protein adhesion when assembled as self-assembled monolayers on gold-coated surfaces and (ii) that the immobilization of these motifs changes …

Fisheries Research Report No. 184 - Macroscopic And Microscopic Description Of Snapper (Pagrus Auratus) Gonads From Shark Bay, Western Australia, Michael C. Mackie, Gary Jackson, Nadia E. Tapp, Jeffrey V. Norriss, Adrian Thomson

Fisheries Research Reports

Since 1997, research on snapper (Pagrus auratus, Sparidae) in the inner gulfs of Shark Bay has focussed on providing biological information required for the management of the regionally important recreational fishery. A major component of this research has been a comprehensive investigation of snapper reproductive biology to determine size and age at maturity, the timing of the spawning season and to estimate batch fecundity. This research has necessitated a review of the macroscopic staging system used for P. auratus in Western Australian waters and the development of a more detailed microscopic system to allow accurate analyses of histological material. Based …

Sonication Assisted Synthesis Of Oligomannosides, Christabel Tomla Tanifum

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Oligomannosides prevalently exist as cell surface antigens. They play important roles in diseases such as viral infection and cancer, and they have been shown to be useful as candidates for vaccines. HIV, one of the most devastating modern diseases, has a high content of mannose sugars on its envelope glycoprotein gp120. Oligomannosides of the HIV virus, also called Man9, which are found on the glycoprotein gp120, have been shown to play a protective role for the HIV virus, shielding highly conserved protein domains of gp120 from proteolytic attacks. Thus gp120 plays an important role in HIV infection of cells, being …

Joint Multiple Testing Procedures For Graphical Model Selection With Applications To Biological Networks, Houston N. Gilbert, Mark J. Van Der Laan, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Gaussian graphical models have become popular tools for identifying relationships between genes when analyzing microarray expression data. In the classical undirected Gaussian graphical model setting, conditional independence relationships can be inferred from partial correlations obtained from the concentration matrix (= inverse covariance matrix) when the sample size n exceeds the number of parameters p which need to estimated. In situations where n < p, another approach to graphical model estimation may rely on calculating unconditional (zero-order) and first-order partial correlations. In these settings, the goal is to identify a lower-order conditional independence graph, sometimes referred to as a ‘0-1 graphs’. For either choice of graph, model selection may involve a multiple testing problem, in which edges in a graph are drawn only after rejecting hypotheses involving (saturated or lower-order) partial correlation parameters. Most multiple testing procedures applied in previously proposed graphical model selection algorithms rely on standard, marginal testing methods which do not take into account the joint distribution of the test statistics derived from (partial) correlations. We propose and implement a multiple testing framework useful when testing for edge inclusion during graphical model selection. Two features of our methodology include (i) a computationally efficient and asymptotically valid test statistics joint null distribution derived from influence curves for correlation-based parameters, and (ii) the application of empirical Bayes joint multiple testing procedures which can effectively control a variety of popular Type I error rates by incorpo- rating joint null distributions such as those described here (Dudoit and van der Laan, 2008). Using a dataset from Arabidopsis thaliana, we observe that the use of more sophisticated, modular approaches to multiple testing allows one to identify greater numbers of edges when approximating an undirected graphical model using a 0-1 graph. Our framework may also be extended to edge testing algorithms for other types of graphical models (e.g., for classical undirected, bidirected, and directed acyclic graphs).

Fisheries Research Report No. 187 - Management And Monitoring Of Fish Spawning Aggregations Within The West Coast Bioregion Of Western Australia, Michael C. Mackie

Fisheries Research Reports

Final FRDC Report – Project Number 2004/051

Objectives

1. To identify species that aggregate to spawn within the WCB and to describe (e.g. location, size, timing, nature) the aggregations of key demersal species such as pink snapper and dhufish.

2. To investigate the biology, ecology and fishery for Samson fish with emphasis on the sports fishery targeting deep water spawning aggregations west of Rottnest Island.

3. To establish methods and protocols for monitoring fish aggregations within the WCB.

4. To review relevant information and provide advice on the impact of aggregation fishing and the management of aggregating fish species in …

Isolation And Characterization Of Aromatase Inhibitors From Brassaiopsis Glomerulata (Araliaceae), Marcy J. Balunas, Bin Su, Soedarsono Riswan, Harry H.S. Fong, Robert W. Brueggemeier, John M. Pezzuto, A. Douglas Kinghorn

Chemistry Faculty Publications

The hexane- and ethyl acetate-soluble extracts of the leaves of Brassaiopsis glomerulata (Blume) Regel (Araliaceae), collected in Indonesia, were found to inhibit aromatase, the rate-limiting enzyme in the production of estrogens from androgens, in both enzyme- and cell-based aromatase inhibition (AI) assays. Bioassay-guided fractionation led to the isolation of six known compounds of the steroid and triterpenoid classes (1–6) from the hexane extract, of which 6β-hydroxystimasta-4-en-3-one (5), was moderately active in the cell-based AI assay. Fractionation of the ethyl acetate extract afforded seven pure isolates (7–13) of the modified peptide, fatty acid, monoterpenoid, and benzenoid types, including six known compounds …

Modeling Thip;Ate Enzyme Chemistry With Cysteine At A High Ph, Emily Michelle Turner

Mahurin Honors College Capstone Experience/Thesis Projects

Thiolate is a highly reactive species critical to the function of many enzymes. We attempted to model the chemistry of two of these enzymes with cysteine in solution at a high pH. To study cysteine proteases, we increased the pH of a cysteine and 4- nitrophenylacetate solution to create a visible color change when thiolyzed that was monitored through UV-Vis spectroscopy to determine rate constants. To study transferases, we attempted to model two reactions. The first was a methyl transfer from guanine to cysteine which mimicked O6-alkylguanine-DNA alkyltransferase. The second was activation of halogenated hydrocarbons by a mechanism similar to …

Insights Into The Population Structure Of Blue Whales In The Eastern North Pacific From Recent Sightings And Photographic Identification, John Calambokidis, Jay Barlow, John K. B. Ford, Todd E. Chandler, Annie B. Douglas

United States Department of Commerce: Staff Publications

Blue whales were widely distributed in the North Pacific prior to the primary period of modern commercial whaling in the early 1900s. Despite concentrations of blue whale catches off British Columbia and in the Gulf of Alaska, there had been few documented sightings in these areas since whaling for blue whales ended in 1965. In contrast, large concentrations of blue whales have been documented off California and Baja California and in the eastern tropical Pacific since the 1970s, but it was not known if these animals were part of the same population that previously ranged into Alaskan waters. We document …

A Locus-Based Paradigm For Generating Systems Biological Inferences From Large Scale Functional Genomics Datasets, Ajish Dominic George

Legacy Theses & Dissertations (2009 - 2024)

Genomics data is growing at a exponential rate. The ability to integrate new results with existing knowledge about genomic biology is rapidly becoming the limiting factor as there no universal language with which to describe genomic functional elements. To integrate and compare new and existing genomic data, we define our basic functional unit of a genome to be a locus -- a set of positional coordinates along any genome with an arbitrary amount of functional annotations attached. The locus concept enables addressing genomic elements and annotations at any level of granularity from entire swaths of chromosomes to single base-positions. We …

Dna Sequence Representation By Use Of Statistical Finite Automata, Asmi Shah

Master's Projects

This project defines and intends to solve the problem of representing information carried by DNA sequences in terms of amino acids, through application of the theory of finite automata. Sequences can be compared against each other to find existing patterns, if any, which may include important genetic information. Comparison can state whether the DNA sequences belong to the same, related or entirely different species in the ‘Tree of Life’ (phylogeny). This is achieved by using extended and statistical finite automata. In order to solve this problem, the concepts of automata and their extension, i.e. Alergia algorithm have been used. In …

Design, Synthesis, And Characterization Of Novel Hydrophilic Fluorene-Based Derivatives For Bioimaging Applications, Dao Nguyen

Electronic Theses and Dissertations

In this work, hydrophilic fluorene-based derivatives that contain ethylene oxide substituents, have been synthesized and characterized for potential use as new fluorophores for bioimaging applications and for fluorescence sensing of heavy metals. Symmetrical and unsymmetrical fluorene derivatives based on structural types of acceptor-pi-acceptor, acceptor-pi-donor, and donor-pi-donor were characterized by TGA, UV-vis absorption, fluorescence emission, lifetime, anisotropy, and two-photon absorption (2PA) cross section. They were found to possess high thermal stability, high photostability, high fluorescence quantum yields, and generally large two-photon absorption cross sections, making them quite suitable for new probes in single-photon absorption and two-photon absorption fluorescence microscopy imaging. Novel …

Preparation Of The Chinese Sweet Leaf Tea Extract And Its Anti-Obesity Effect In Rodents, Gar Yee Koh

LSU Master's Theses

The aqueous leaf extract of Rubus suavissimus (Chinese sweet leaf tea) was active in inhibiting angiogenesis, which could be used to suppress adipogenesis and cause weight loss. Following this revelation and approach, the anti-obesity effect was thoroughly investigated in normal and obese rat models. The investigations began with the preparation of quality-controlled extract. First, the crude extraction methods were examined leading to the characterization of the chemical composition. Second, the impure components were removed by alcohol precipitation and column chromatography, resulting in a standardized sweet leaf tea extract (RUS). Third, three bioavailable compounds identified from the urine analyses were re-constituted …

Investigation And Quantification Of Codon Usage Bias Trends In Prokaryotes, Amanda L. Hanes

Browse all Theses and Dissertations

Organisms construct proteins out of individual amino acids using instructions encoded in the nucleotide sequence of a DNA molecule. The genetic code associates combinations of three nucleotides, called codons, with every amino acid. Most amino acids are associated with multiple synonymous codons, but although they result in the same amino acid and thus have no effect on the final protein, synonymous codons are not present in equal amounts in the genomes of most organisms. This phenomenon is known as codon usage bias, and the literature has shown that all organisms display a unique pattern of codon usage. Research also suggests …

Noncovalent Interaction Of Platinum Planar Amine Compounds With Tryptophan: A Strategy To Interfere With P53-Mdm2 Interactions And Targeting Retroviral Zn Finger-Dna Interaction (Hiv Ncp7), Aaron Bate

Theses and Dissertations

Non-covalent interactions involving π-π stacking play an essential role in self-assembly and molecular recognition processes such as protein folding and DNA/RNA-protein selective recognition. The knowledge gained from these studies could provide insight into possible site recognition complexes, inhibiting or mimicking protein-protein or protein-DNA interactions. Based on molecular modeling as well as HOMO and LUMO energies, several chromophores were selected with a variety of ∆ε values (∆ε= |εHOMO,NAcTrp – εLUMO,chromophores|), high and low, to establish a correlating trend with the modeling and experimental data. The corresponding Pt(dien) compounds were synthesized and their ability to stack to N-acetyl tryptophan was evaluated by …

Bottom Boundary Layer Physics And Sediment Transport Along A Transgressive Sand Body, Ship Shoal, South-Central Louisiana: Implications For Fluvial Sediments And Winter Storms, Daijiro Kobashi

LSU Doctoral Dissertations

Ship Shoal, a shore-parallel sand body, was recently recognized as having a unique physical and biological environment and also as a potential sand resource for coastal restoration in coastal Louisiana. Little is known regarding such dynamics, in concert with fluvial sediments and winter storms, influenced in unique ecosystems, and likely in future potential sand mining. This dissertation addresses such the morphodynamics and sedimentary processes and their implications for the mining from the shoal using field measurements and numerical modeling studies. During the winter-spring season, fluvial sediment plumes shifted from the prevailing west to southeast during the post-frontal phases, resulted in …

Highly Stereoselective B-Lactam Synthesis Via The Staudinger Reaction Using Poly Aromatic Imines, Debasish Bandyopadhyay, Monica Xavier, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Highly stereoselective synthesis of a few trans 3-phthalimido substituted B-lactams has been achieved following Staudinger reaction.

“Species Pollution” In Florida: A Cross-Section Of Invasive Vertebrate Issues And Management Responses, Richard M. Engeman, Bernice Constantin, Scott Hardin, Henry Smith, Walter Meshaka Jr.

United States Department of Agriculture Wildlife Services: Staff Publications

The state of Florida as among the two worst invasive species problems in the USA. Besides the sheer numbers of established exotic species in Florida, many present novel difficulties for management, or have other characteristics making effective management extremely challenging. Moreover, initiation of management action requires more than recognition by experts that a potentially harmful species has become established. It also requires the political will along with concomitant resources and appropriate personnel to develop effective methods and apply them. We illustrate various aspects of the situation in Florida with examples of invasive vertebrates, the problems they pose(d), and management approaches …

Limnological Assistance For The Lake Mead National Recreation Area In Meeting The Challenge Of The Water 2025 Initiative: Quarterly Report, Period Ending September 30, 2008, Margaret N. Rees

Limnological Studies

Project 1: Technical input has been provided at eight advisory team meetings attended this quarter. Broad, overarching “Issues of Concern” developed for the Boulder Basin Adaptive Management Plan are currently under review by Drs. David Wong and Shawn Gerstenberger. A Selenium Management Plan is also under review.

Project 2: Data collected by the Southern Nevada Water Authority has been synthesized to summarize bacteria counts in high-use areas of Lakes Mead and Mohave. This information will be documented and interpreted for management use in a formal report in the upcoming quarter.

Project 3: A draft document titled “Suggested Standard Methods for …

Ground-Penetrating Radar And Thermal Modeling Of Active Layer Thaw Beneath Arctic Streams, Troy Richard Brosten

Boise State University Theses and Dissertations

Seasonal thaw depth beneath arctic streams significantly impacts physical and biological processes within arctic stream environments. The impact of greater seasonal thaw for extended periods of time can alter ecosystems that have, in the past, resulted from more prevalent permafrost environments. Effects of climatic change on arctic stream environments necessitate the need for more information on characteristics of seasonal thaw and processes that occur within the thawed layer. Multiple ground-penetrating radar (GPR) methods and one-dimensional (1D) thermal modeling were used to investigate seasonal thaw beneath arctic streams and determine the dominant thermal process.

Study sites were selected to include stream …

The Beginning Of The End For Chimpanzee Experiments?, Andrew Knight

Experimentation Collection

The advanced sensory, psychological and social abilities of chimpanzees confer upon them a profound ability to suffer when born into unnatural captive environments, or captured from the wild – as many older research chimpanzees once were – and when subsequently subjected to confinement, social disruption, and involuntary participation in potentially harmful biomedical research. Justifications for such research depend primarily on the important contributions advocates claim it has made toward medical advancements. However, a recent large-scale systematic review indicates that invasive chimpanzee experiments rarely provide benefits in excess of their profound animal welfare, bioethical and financial costs. The approval of large …

Geographic Variation In Killer Whale Attacks On Humpback Whales In The North Pacific: Implications For Predation Pressure, Gretchen H. Steiger, John Calambokidis, Janice M. Straley, Louis M. Herman, Salvatore Cerchio, Dan R. Salden, Jorge Urban-R., Jeff K. Jacobsen, Olga Von Ziegesar, Kenneth C. Balcomb, Christine M. Gabriele, Marilyn E. Dahlheim, Senzo Uchida, John K. B. Ford, Paloma Ladron De Guevara-P., Manami Yamaguchi, Jay Barlow

United States Department of Commerce: Staff Publications

We examined the incidence of rake mark scars from killer whales Orcinus orca on the flukes of humpback whales Megaptera novaeangliae throughout the North Pacific to assess geo- graphic variation in predation pressure. We used 3650 identification photographs from 16 wintering or feeding areas collected during 1990 to 1993 to determine conservative estimates in the percentage of whales with rake mark scarring. Dramatic differences were seen in the incidence of rake marks among regions, with highest rates on wintering grounds off Mexico (26 vs. 14 % at others) and feeding areas off California (20 vs. 6% at others), 2 areas …

Synthetic Studies And Biological Evaluation Of Imidazole-Containing Marine Alkaloids, Lesley Ann Schmid

Chemistry & Biochemistry Dissertations - Archive

This dissertation discusses the synthetic methods towards and the preliminary biological studies of an unnamed, imidazole-containing alkaloid, derived from the marine species Oceanapia. This alkaloid was first discovered in 1996 by researchers at the NIH as a possible inhibitor of the key enzyme in the detoxification cycle of Mycobacterium tuberculosis. Chapter 1 provides an overview of tuberculosis, which is currently the second highest cause of death worldwide, with one third of the world's population infected. In recent years, the emergence of multi-drug resistant strains has created new interest and funding for tuberculosis research. New treatments like the alkaloid described above …

Carbon, Nitrogen, Sodium And Phosphorous Concentrations And Ratios In Spartina Alterniflora (Loiser) From Sites Of Various Freshwater And Nutrient Inputs In Coastal Louisiana Wetlands, Margaret Frances Williamson

Honors Capstones

No abstract provided.

Methods Development In Qualitative And Quantitative Proteomics, Ting Liu

University of Kentucky Doctoral Dissertations

Proteomics based on liquid chromatography coupled to mass spectrometry has developed rapidly in the last decade and become a powerful tool for protein mixtures analysis. LC-MS based proteomics involves four steps, sample preparation, liquid chromatography, mass spectrometry and bioinformatics. Improvements in each step have extended its applications to new biological research areas. This dissertation mainly focuses on method developments in both qualitative and quantitative proteomics.

The first part of this dissertation focuses on qualitative analysis of T. gondii Parasitophorous Vacuole Membrane (PVM) proteins, which is very important for T. gondii’s survival. The hypothesis of this study is that proteomic …

Interagency Science And Research Strategy, Limnological Assistance For Lake Mead National Recreation Area

Limnological Studies

Helping improve operational efficiency, enhance land stewardship, resource protection, and conservation on the shared public land.

Dms Air/Sea Flux And Gas Transfer Coefficients From The North Atlantic Summertime Coccolithophore Bloom, Christa Marandino, Warren J. De Bruyn, Scott Miller, Eric S. Saltzman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Dimethylsulfide (DMS) atmospheric and oceanic concentrations and eddy covariance air/sea fluxes were measured over the N. Atlantic Ocean during July 2007 from Iceland to Woods Hole, MA, USA. Seawater DMS levels north of 55 degrees N ranged from 3 to 17 nM, with variability related to the satellite-derived distributions of coccoliths and to a lesser extent, chlorophyll. For the most intense bloom region southwest of Iceland, DMS air/sea fluxes were as high as 300 mu mol m(-2) d(-1), larger than current model estimates. The observations imply that gas exchange coefficients in this region are significantly greater than those estimated using …

Alayzing The Effects Of Modularity On Search Spaces, Ozlem Garibay

Electronic Theses and Dissertations

We are continuously challenged by ever increasing problem complexity and the need to develop algorithms that can solve complex problems and solve them within a reasonable amount of time. Modularity is thought to reduce problem complexity by decomposing large problems into smaller and less complex subproblems. In practice, introducing modularity into evolutionary algorithm representations appears to improve search performance; however, how and why modularity improves performance is not well understood. In this thesis, we seek to better understand the effects of modularity on search. In particular, what are the effects of module creation on the search space structure and how …

The Impact Of Nutrient Availability And Algal Community On Carbon Isotope Fractionaion In Crystal Lake, Clark County, Ohio, April R. Wisebaker

Browse all Theses and Dissertations

Crystal Lakes are a group of four interconnected lakes, located in southwestern Clark County, Ohio. Several studies have looked at separate geochemical and isotopic information at this location. However, no one has thoroughly studied the relationship between the algal community, geochemistry, and carbon isotope fractionation within Crystal Lake. The fractionation of carbon isotopes of dissolved inorganic carbonate is greatly affected by the process of photosynthesis; the amount of photosynthesis is affected by the amount of algae in the aquatic community; the amount of algae is affected by the available nutrients in system. Therefore, there should be a correlation between the …

Algorithmic Techniques Employed In The Isolation Of Codon Usage Biases In Prokaryotic Genomes, Douglas W. Raiford Iii

Browse all Theses and Dissertations

While genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Isolation of translational efficiency bias can have important …

Evanescent Microwave Microscopy Of Porcine Skin Tissue, Richard A. Kleismit

Browse all Theses and Dissertations

This thesis describes the application of a custom designed λ/4 resonant coaxial probe to measurements of the complex permittivity of in vitro freshly excised porcine skin tissue. The dielectric properties of the organic material within the near field of the tip of the probe frustrates the electric field and measurably changes the resonant frequency and quality factor Q of the coaxial sensor, where the change in resonant frequency and quality factor of a tuned resonance is measured as a function of tip-sample separation. The design of the probe enables better spatial resolution than previously developed probes. The following studies were …