Life Sciences Commons^™

Fluorescence And Size Characterization Of Dissolved Organic Matter In Riverine And Sea Waters In The Northern Gulf Of Mexico, Zhengzhen Zhou

Dissertations

Riverine export of dissolved organic matter (DOM) is an important component in marine carbon budget but the composition and phase partitioning are poorly quantified. Monthly water samples were collected from the lower Mississippi and Pearl rivers between January 2009 to August 2011 for DOM characterization using the fluorescence excitation emission matrix (FluoEEM) technique, coupled with parallel factor analysis (PARAFAC), and flow field-flow fractionation technique. DOM in the Pearl River showed higher dissolved organic carbon (DOC) concentration, temporal fluctuation, and aromaticity, reflecting instantaneous inputs of DOM from local soil and plant litter. In contrast, DOM in the Mississippi River exhibited lower …

The Role Of The Cysteine/Glutathione Regulatory Genes Cdo1, Gsh1, And Gsh2 In Yeast-Mold Dimorphism Of The Pathogenic Fungus Histoplasma Capsulatum, Melissa Anne Adams

Dissertations

The dimorphism of Histoplasma capsulatum (Hc) from a mold to yeast is regulated by many environmental factors such as temperature and thiol concentrations. Histoplasma exists in the soil (or in vitro at 25ºC) as a multicellular saprophytic mold. In the lungs of an infected host (or in vitro at 37ºC), a shift to the unicellular parasitic yeast occurs. Sulfhydryl groups (-SH), especially cysteine, are necessary in the culture medium for the mold to yeast transition. Cysteine is the precursor for the synthesis of glutathione. Enzymes involved in the cysteine metabolism pathway are being studied in order to evaluate …

Characterisation Of Pharmaceutical Grade Horse Chestnut Waste, Joanna Przyborska

Theses

Horse chestnut residue was made available by a local pharmaceutical company. The residue was subjected to compositional analysis and studied to determine potential for residual biological activity, including prebiotic, antimicrobial, anti-hyaluronidase and anti-elastase effects.

The residue had 52 % total solids, including 2.97% ash, 6.93% protein, 1.89% crude fat. Oleic acid (74.7%) was the main fatty acid components in the crude lipid component. The major ash components were potassium, phosphorus, calcium and magnesium.

Prebiotic potential of aqueous extract (HCE) from horse chestnut residue was confirmed. A new formula for calculation of prebiotic index (PI) was developed. PI for probiotics (Lactobacillus …

B-Cell Epitope Prediction Through A Graph Model, Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven C. H. Hoi, Jinyan Li

Research Collection School Of Computing and Information Systems

Prediction of B-cell epitopes from antigens is useful to understand the immune basis of antibody-antigen recognition, and is helpful in vaccine design and drug development. Tremendous efforts have been devoted to this long-studied problem, however, existing methods have at least two common limitations. One is that they only favor prediction of those epitopes with protrusive conformations, but show poor performance in dealing with planar epitopes. The other limit is that they predict all of the antigenic residues of an antigen as belonging to one single epitope even when multiple non-overlapping epitopes of an antigen exist.

Understanding The Tradeoff Between Safety And Food Quality In A Mammalian Herbivore Specialist, The Pygmy Rabbit, Jamie Lyn Utz

Boise State University Theses and Dissertations

Conserving a sensitive animal species requires understanding the simultaneous tradeoffs between food and shelter within a landscape. Most management approaches only consider single factors like percent cover at landscape spatial scales. Quantifying the synergy between cover and food quality at a scale relevant to a foraging animal could better reveal the forces that shape habitat use. To better understand habitat use components, I investigated tradeoffs between predation risk and diet quality in a sagebrush endemic, the pygmy rabbit (Brachylagus idahoensis). This species is a rare example of a specialist herbivore that relies almost entirely on sagebrush for cover …

An Examination Of Finish Time Variation For Collegiate Cross Country National Championships By Gender, Kevin Riley Peters

Boise State University Theses and Dissertations

In cross country, women compete over shorter distances than men with little justification for these differences. The purpose of this study was to assess gender differences for the spread of finishing times and examine the appropriateness of shorter competition distances for females. Forty-six cross country national championship data sets (n_males = 10,788; n_females = 10,884) from the NCAA (1999-2011) and NAIA (2005-2011) were utilized for analyses. Several measures of variation were computed to assess spread of finishing times data (i.e., Coefficient of Variation [CV]; Interpercentile Ranges [IR], and Rates of Separation [RS; IR divided by the distance …

Tumour Inflammasome-Derived Il-1b Recruits Neutrophils And Improves Local Recurrence-Free Survival In Ebv-Induced Nasopharyngeal Carcinoma, Lih-Chyang Chen, Li-Jie Wang, Nang-Ming Tsang, David M. Ojcius, Chia-Chen Chen, Chun-Nan Ouyang, Chuen Hsueh, Ying Liang, Kai-Ping Chang, Chiu-Chin Chen, Yu-Sun Chang

All Dugoni School of Dentistry Faculty Articles

Inflammasomes sense infection and cellular damage and are critical for triggering inflammation through IL-1β production. In carcinogenesis, inflammasomes may have contradictory roles through facilitating antitumour immunity and inducing oncogenic factors. Their function in cancer remains poorly characterized. Here we show that the NLRP3, AIM2 and RIG-I inflammasomes are overexpressed in Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC), and expression levels correlate with patient survival. In tumour cells, AIM2 and RIG-I are required for IL-1β induction by EBV genomic DNA and EBV-encoded small RNAs, respectively, while NLRP3 responds to extracellular ATP and reactive oxygen species. Irradiation and chemotherapy can further activate AIM2 …

Reversible Inhibition Of Chlamydia Trachomatis Infection In Epithelial Cells Due To Stimulation Of P2x4 Receptors, Matthew A. Pettengill, Camila Marques-Da-Silva, Maria Luisa Avila, Verissa W. Lam, Ikechukwu Ollawa, Ali Abdul-Sater, Robson Coutinho-Silva, Georg Hacker, David M. Ojcius, Suellen D'Arc Dos Santos Oliveira

All Dugoni School of Dentistry Faculty Articles

Bacterial infections of the mucosal epithelium are a major cause of human disease. The prolonged presence of microbial pathogens stimulates inflammation of the local tissues, which leads to changes in the molecular composition of the extracellular milieu. A well-characterized molecule that is released to the extracellular milieu by stressed or infected cells is extracellular ATP and its ecto-enzymatic degradation products, which function as signaling molecules through ligation of purinergic receptors. There has been little information, however, on the effects of the extracellular metabolites on bacterial growth in inflamed tissues. Millimolar concentrations of ATP have been previously shown to inhibit irreversibly …

Resistance Is Futile: The Bacteriocin Model For Addressing The Antibiotic Resistance Challenge, Margaret A. Riley, Sandra M. Robinson, Christopher M. Roy, Morgan Dennis, Vivian Liu, Robert Dorit

Biological Sciences: Faculty Publications

Pathogenic bacteria resistant to many or all antibiotics already exist. With the decline in microbiological research at pharmaceutical companies, the high rate at which resistance has evolved and spread has demanded a novel approach to addressing this critical human health issue. In the present paper, we propose a new paradigm in antibiotic discovery and development, one that applies ecological and evolutionary theory to design antimicrobial drugs that are more difficult and/or more costly to resist. In essence, we propose to simply adopt the strategies invented and applied by bacteria for hundreds of millions of years. Our research focuses on bacteriocins, …

Regulation Of Alternative Carbon Metabolism In Candida Albicans, Arely Y. Gonzalez

Dissertations and Theses (Open Access)

Candida albicans is the most important fungal pathogen of humans. Transcript profiling studies show that upon phagocytosis by macrophages, C. albicans undergoes a massive metabolic reorganization activating genes involved in alternative carbon metabolism, including the glyoxylate cycle, β-oxidation and gluconeogenesis. Mutations in key enzymes such as ICL1 (glyoxylate cycle) and FOX2 (fatty acid β-oxidation) revealed that alternative carbon metabolic pathways are required for full virulence in C. albicans. These studies indicate C. albicans uses non-preferred carbon sources allowing its adaptation to microenvironments were nutrients are scarce. It has become apparent that the regulatory networks required for regulation of alternative …

Identifying Genetic Variants And Characterizing Their Role In Clubfoot, Katelyn S. Weymouth

Dissertations and Theses (Open Access)

Clubfoot is a common, complex birth defect affecting 4,000 newborns in the United States and 135,000 world-wide each year. The clubfoot deformity is characterized by inward and rigid downward displacement of one or both feet, along with persistent calf muscle hypoplasia. Despite strong evidence for a genetic liability, there is a limited understanding of the genetic and environmental factors contributing to the etiology of clubfoot. The studies described in this dissertation were performed to identify variants and/or genes associated with clubfoot. Genome-wide linkage scan performed on ten multiplex clubfoot families identified seven new chromosomal regions that provide new areas to …

Biogenic Amine Levels Correlate With Time Of Day, Age, Light Cycle, And Aggressive State In The Flesh Fly, Sarcophaga Crassipalpis, Veronica L. Fregoso

Electronic Theses and Dissertations

The biogenic amines serotonin (5HT), dopamine (DA), and octopamine (OA) have been indicated in the regulation of behaviors, including aggression. The flesh fly, Sarcophaga crassipalpis, was used to investigate ontogenetic and circadian changes in amines and aggression. Heads of male flies were analyzed for amine content using high performance liquid chromatography with electrochemical detection (HPLC-ECD) at 3 time points on each of 4 consecutive days in 2 light cycles, 12:12 LD and 15:9 LD. Both DA and OA levels decreased with age. Light-cycle dependent differences were observed for all amines in overall levels and patterns of change throughout the …

Differential Surface Deposition Of Complement Proteins On Logarithmic And Stationary Phase Leishmania Chagasi Promastigotes, Amanda Ramer-Tait, Soi Meng Lei, Bryan H. Bellaire, Jeffrey K. Beetham

Department of Food Science and Technology: Faculty Publications

Previous works demonstrated that various species of Leishmania promastigotes exhibit differential sensitivity to complement-mediated lysis (CML) during development. Upon exposure to normal human serum (NHS), cultures of Leishmania chagasi promastigotes recently isolated from infected hamsters (fewer than 5 in vitro passages) are CML-sensitive when in the logarithmic growth phase but become CML-resistant upon transition to the stationary culture phase. Visualization by light and electron microscopy revealed dramatic morphological differences between promastigotes from the 2 culture phases following exposure to NHS. Flow cytometric analysis demonstrated that surface deposition of the complement components C3, C5, and C9 correlated inversely with promastigote CML-resistance. …

Spectrum Of Acute Clinical Characteristics Of Diagnosed Concussions In College Athletes Wearing Instrumented Helmets, Ann-Christine Duhaime,, Jonathan G. Beckwith, Arthur C. Maerlender, Thomas W. Mcallister, Joseph J. Crisco, Stefan M. Duma, P. Gunnar Brolinson, Steven Rowson, Laura A. Flashman, Jeffrey J. Chu, Richard M. Greenwald

Department of Psychology: Faculty Publications

Object. Concussive head injuries have received much attention in the medical and public arenas, as concerns have been raised about the potential shortand long-term consequences of injuries sustained in sports and other activities. While many student athletes have required evaluation after concussion, the exact definition of concussion has varied among disciplines and over time. The authors used data gathered as part of a multiinstitutional longitudinal study of the biomechanics of head impacts in helmeted collegiate athletes to characterize what signs, symptoms, and clinical histories were used to designate players as having sustained concussions.

Methods. Players on 3 college …

Mortality Assessment Of Redwood And Mixed Conifer Forest Types In Santa Cruz County Following Wildfire, Steve R. Auten

Master's Theses

On August 12, 2009, the Lockheed Fire ignited the west slope of the Santa Cruz Mountains burning approximately 7,819 acres. Foresters and other land managers were left with challenging decisions on how to evaluate tree mortality. Big Creek Lumber Company, California Polytechnic State University, San Luis Obispo (Cal Poly)’s Swanton Pacific Ranch (SPR), and other resource professionals familiar with this region teamed up to develop a method for evaluating damage and thereby mortality for redwood, California nutmeg, live oak, tanoak, California bay, Pacific madrone, big leaf maple, Douglas-fir, Monterey pine, and knobcone pine. Quantitative damage criteria were used to design …

Post-Fire Mortality And Response In A Redwood/ Douglas-Fir Forest, Santa Cruz Mountains, California, Garren M. Andrews

Master's Theses

We investigated how fire severity impacts the survival and response (sprouting/seeding) of multiple species in the Santa Cruz Mountains of coastal California, including coast redwood (Sequoia sempervirens), Douglas-fir (Pseudotsuga menziesii), tanoak (Lithocarpus densiflorus), and Pacific madrone(Arbutus menziesii). During August 2009 the Lockheed Fire burned nearly 3,160ha of mixed-conifer stands with variable severity. Data from 37 Continuous Forest Inventory (CFI) plots were collected immediately before and for 2 successive years following the 2009 Lockheed Fire.

This research entails three objectives. First, we quantified post-fire mortality of trees that vary in species, size, and …

Low Cost Neurochairs, Frankie Pike

Master's Theses

Electroencephalography (EEG) was formerly confined to clinical and research settings with the necessary hardware costing thousands of dollars. In the last five years a number of companies have produced simple electroencephalograms, priced below $300 and available direct to consumers. These have stirred the imaginations of enthusiasts and brought the prospects of "thought-controlled" devices ever closer to reality. While these new devices were largely targeted at video games and toys, active research on enabling people suffering from debilitating diseases to control wheelchairs was being pursued. A number of neurochairs have come to fruition offering a truly hands-free mobility solution, but whether …

House Finches, Carpodacus Mexicanus: Hormones, Stress, And Song Control Regions, Katherine Olivia Ganster

Master's Theses

Song production in songbirds is controlled by parts of the brain known as the song control regions (SCRs). During spring, gonads increase in size, males sing to attract mates, and SCRs become larger. This neuroplasticity is controlled by the change in day length and increased plasma testosterone (T) levels. Plasma T can be reduced by stress through the production of corticosterone (CORT), through the production of beta-endorphin, or through direct effects on the testes via the nervous system. We determined the T, estradiol, and CORT hormonal profiles of wild House Finches by capturing and sampling blood from the finches every …

Histologic Findings In Biopsies/Resection Specimens From The Small Intestine With Special Emphasis On Celiac Disease: Experience From A Developing Country In South Asia, Huma Arshad, Zubair Ahmad

Department of Pathology and Laboratory Medicine

Biopsies from the small intestine especially the duodenum are now being performed much more frequently than in the past. The most frequent reason for performing duodenal biopsies is to evaluate for malabsorption. In the last few years, increased awareness has resulted in more biopsies sent for evaluation of malabsorption, especially celiac disease (CD). In the duodenum, features of malabsorption (increased intraepithelial lymphocytes, villous shortening, and atrophy) were the most common histologic finding seen in 63.4% of cases. Serum tTG levels were available for correlation in 52.8% of cases. In patients with confirmed CD, 53.4% were MARSH IIIb, and 29.5% were …

Sensitivity Of The Wolf’S And Rosenstein’S Algorithms To Evaluate Local Dynamic Stability From Small Gait Data Sets: Response To Commentaries By Bruijn Et Al., Fabien Cignetti, Leslie M. Decker, Nikolaos Stergiou

Journal Articles

Assessing gait stability using the Largest Lyapunov Exponent (λ₁) has become popular, especially because it may be a key measure in evaluating gait abnormalities in patient populations. However, clinical settings usually involve having small gait data sets and accurate determination of λ₁ estimates from such sets is difficult. In an effort to address this issue, Cignetti et al.2 recently identified that λ₁ estimates using the algorithm of Wolf et al.9 (W-algorithm) were more sensitive than those using the algorithm of Rosenstein et al.7 (R-algorithm) in order to capture age-related …

Peripheral Arterial Disease Affects The Frequency Response Of Ground Reaction Forces During Walking, Denise Mcgrath, Timothy N. Judkins, Iraklis Pipinos, Jason Johanning

Journal Articles

Background—Walking is problematic for patients with Peripheral Arterial Disease. The purpose of this study was to investigate the frequency domain of the ground reaction forces during walking to further elucidate the ambulatory impairment of these patients.

Methods—Nineteen bilateral peripheral arterial disease patients and nineteen controls were included in this study. Subjects were matched for age and gait speed. Participants walked over a force plate sampling at 600Hz. PAD patients were tested before (pain-free condition) after the onset of claudication symptoms (pain). We calculated median frequency, frequency bandwidth, and frequency containing 99.5% of the signal for the vertical and …

Molecular Phylogeny Of Microhylid Frogs (Anura: Microhylidae) With Emphasis On Relationships Among New World Genera, Rafael O. De Sá, Jeffrey W. Streicher, Relebohile Sekonyela, Mauricio C. Forlani, Simon P. Loader, Eli Greenbaum, Stephen Richards, Célio F.B. Haddad

Biology Faculty Publications

Background: Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis).

Results: One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an …

Genetic Analysis Of The Hippo Pathway In Mouse Liver, Li Lu

Dissertations and Theses (Open Access)

Cancer therapy and tumor treatment remain unsolved puzzles. Genetic screening for tumor suppressor genes in Drosophila revealed the Hippo-signaling pathway as a kinase cascade consisting of five core components. Disrupting the pathway by deleting the main component genes breaks the balance of cell proliferation and apoptosis and results in epithelial tissue tumorigenesis. The pathway is therefore believed to be a tumor suppressor pathway. However, a corresponding role in mammals is yet to be determined. Our lab began to investigate the tumor suppression function of the potent mammalian Hippo pathway by putting floxed alleles into the mouse genome flanking the functional-domain-expressing …

Prostate Cancer Stem Cells: Drug To Lerance, Experimental Reconstitution And Castration Resistance, Xin Chen

Dissertations and Theses (Open Access)

Prostate cancer (PCa) is one of the leading malignancies affecting men in the Western world. Although tremendous effort has been made towards understanding PCa development and developing clinical treatments in the past decades, the exact mechanisms of PCa are still not clearly understood. Emerging evidence has postulated that a population of stem cell-like cells inside a tumor, termed ‘cancer stem cells (CSCs)’, may be the cells responsible for tumor initiation, progression, recurrence, metastasis and therapy resistance. Like CSC studies in other cancer types, it has been reported that PCa also contains CSCs. However, there remain several unresolved questions that need …

Mutations In Stat3 Associated With Human Hyper Ige Syndrome Enhance Nfκb And Mapk-Mediated Gene Expression, Nathaniel Greeley

Dissertations and Theses (Open Access)

Hyper IgE syndrome (HIES) is a multisystem disorder resulting in bone and immune system abnormalities. It is associated with mutations in STAT3, which disrupt protein domains responsible for transcriptional function. Patients with HIES display osteoporosis and enhanced inflammatory cytokine production similar to hematopoietic Stat3-deficient mice. Since osteoclast and inflammatory cytokine genes are NFκB targets, these observations indicate a possible deregulation of NFκB signaling in both mice and humans with STAT3-deficiency. Here, we sought to examine the role of STAT3 in the regulation of NFκB-mediated gene expression through analysis of three HIES STAT3 point mutations in both hematopoietic and non- hematopoietic …

Fancm And Faap24 Maintain Genomic Stability Through Cooperative And Unique Functions, Yucai Wang

Dissertations and Theses (Open Access)

Fanconi anemia (FA) is a rare recessive genetic disease with an array of clinical manifestations including multiple congenital abnormalities, progressive bone marrow failure and profound cancer susceptibility. A hallmark of cells derived from FA patients is hypersensitivity to DNA interstrand crosslinking agents such as mitomycin C (MMC) and cisplatin, suggesting that FA- and FA-associated proteins play important roles in protecting cells from DNA interstrand crosslink (ICL) damage. Two genes involved in the FA pathway, FANCM and FAAP24, are of particular interest because they contain DNA interacting domains. However, there are no definitive patient mutations for these two genes, and the …

Anti-Tumor Effects Of The Notch Pathway In Gastrointestinal Stromal Tumors, Amaury G. Dumont

Dissertations and Theses (Open Access)

Gastrointestinal Stromal Tumors (GIST) are sarcomas driven by gain-of-function mutations of KIT or PDGFRA. Although, the introduction of tyrosine kinase inhibitors has dramatically changed the history of this disease, evidences emerge that inhibition of KIT or PDGFRA are not sufficient to cure patients. The developmental pathway Notch has a critical role in the cell fate, regulating cell proliferation and differentiation. Dysregulation of Notch pathway has been implicated in a wide variety of cancers functioning as a tumor promoter or a tumor suppressor in a cell context dependent manner.

Given that Notch activation deregulates the morphogenesis of mesenchymal cells in …

Genetic Interactions Of Factors That Regulate Alternative Rna Splicing In The Male Germ Line Of Drosophila, Shanzhi Wang

Dissertations and Theses (Open Access)

Alternative RNA splicing is a critical process that contributes variety to protein functions, and further controls cell differentiation and normal development. Although it is known that most eukaryotic genes produce multiple transcripts in which splice site selection is regulated, how RNA binding proteins cooperate to activate and repress specific splice sites is still poorly understood. In addition how the regulation of alternative splicing affects germ cell development is also not well known. In this study, Drosophila Transformer 2 (Tra2) was used as a model to explore both the mechanism of its repressive function on its own pre-mRNA splicing, and the …

Differential Activity Of The Kras Oncogene By Method Of Activation: Implications For Signaling And Therapeutic Intervention, Nathan Ihle

Dissertations and Theses (Open Access)

Despite having been identified over thirty years ago and definitively established as having a critical role in driving tumor growth and predicting for resistance to therapy, the KRAS oncogene remains a target in cancer for which there is no effective treatment. KRas is activated b y mutations at a few sites, primarily amino acid substitutions at codon 12 which promote a constitutively active state. I have found that different amino acid substitutions at codon 12 can activate different KRas downstream signaling pathways, determine clonogenic growth potential and determine patient response to molecularly targeted therapies. Computer modeling of the KRas structure …

The Role Of The Arched Helicases In Exosome-Mediated Function, A. Alejandra Klauer

Dissertations and Theses (Open Access)

RNA processing and degradation are two important functions that control gene expression and promote RNA fidelity in the cell. A major ribonuclease complex, called the exosome, is involved in both of these processes. The exosome is composed of ten essential proteins with only one catalytically active subunit, called Rrp44. While the same ten essential subunits make up both the nuclear and cytoplasmic exosome, there are nuclear and cytoplasmic exosome cofactors that promote specific exosome functions in each of the cell compartments. To date, it is unclear how the exosome distinguishes between RNA substrates. We hypothesize that compartment specific cofactors may …