Life Sciences Commons^™

Towards The Prediction Of Mutations In Genomic Sequences, Juan Carlos Martinez

FIU Electronic Theses and Dissertations

Bio-systems are inherently complex information processing systems. Furthermore, physiological complexities of biological systems limit the formation of a hypothesis in terms of behavior and the ability to test hypothesis. More importantly the identification and classification of mutation in patients are centric topics in today’s cancer research.

Next generation sequencing (NGS) technologies can provide genome-wide coverage at a single nucleotide resolution and at reasonable speed and cost. The unprecedented molecular characterization provided by NGS offers the potential for an individualized approach to treatment. These advances in cancer genomics have enabled scientists to interrogate cancer-specific genomic variants and compare them with the …

Roles Of Dna Base Excision Repair In Maintaining The Integrity Of Dna Methylation, Jing Zhou

FIU Electronic Theses and Dissertations

DNA methylation and demethylation are involved in regulation of gene expression. CpG clusters have been identified as hotspots of oxidative damages and mutagenesis. DNA base excision repair can remove oxidative DNA damage on CpG clusters and mediate an active DNA demethylation pathway. In this study, we examined the molecular mechanisms underlying interactions among DNA methylation, demethylation and BER. Our results demonstrated that a single 5-methylcytosine did not exhibit a significant effect on BER. Surprisingly we found that the abasic site completely inhibited the activity of thymine DNA glycosylase (TDG) leading to the sustainment of the mismatch efficiently extended by pol …

Real-Time Qpcr Assay Development For Detection Of Bacillus Thuringiensis And Serratia Marcescens Dna And The Influence Of Complex Microbial Community Dna On Assay Sensitivity, Jonathan Segal

FIU Electronic Theses and Dissertations

Real-time quantitative polymerase chain reaction (real-time qPCR) assays are an effective technique to detect biological warfare agents and surrogate organisms. In my study, primers were designed to detect chromosomal DNA of biological warfare agent surrogates B. thuringiensis and S. marcescens (representing B. anthracis and Y. pestis, respectively) via real-time qPCR. Species-level specificity of the primers was demonstrated through comparisons with a bacterial strain panel and corroborated by qPCR data. Additionally, the primer efficacy was tested when template DNA was spiked into metagenomic DNA extracted from clinical lung microbiome samples. The results showed that while detection of B. thuringiensis or …

A Novel Signal Processing Method For Intraoperative Neurophysiological Monitoring In Spinal Surgeries, Krishnatej Vedala

FIU Electronic Theses and Dissertations

Intraoperative neurophysiologic monitoring is an integral part of spinal surgeries and involves the recording of somatosensory evoked potentials (SSEP). However, clinical application of IONM still requires anywhere between 200 to 2000 trials to obtain an SSEP signal, which is excessive and introduces a significant delay during surgery to detect a possible neurological damage. The aim of this study is to develop a means to obtain the SSEP using a much less, twelve number of recordings. The preliminary step involved was to distinguish the SSEP with the ongoing brain activity. We first establish that the brain activity is indeed quasi-stationary whereas …

Recreational Angler Perspectives Of Nonnative Fish Species And Mercury Advisories, Christopher J. Edwards

FIU Electronic Theses and Dissertations

The central Everglades serve as a Wildlife Management Area and as a Water Conservation Area for the Miami-Fort Lauderdale metropolitan area. It is also home to over 22 nonnative freshwater fish species and carries restrictive fish consumption guidelines for Mercury. In my study, boat anglers and canal bank anglers were personally interviewed in the field, to research their awareness and perspectives of these potential environmental and health threats. The study found 78% of anglers were aware of the presence of nonnative fish species, but favored native fish species, and that 69% were aware of mercury advisories, but did not eat …

Investigating The In Vitro Oxidative Folding Pathways Of Bovine Pancreatic Trypsin Inhibitor (Bpti), Yingsong Wang

FIU Electronic Theses and Dissertations

The oxidative folding pathway of the disulfide containing protein bovine pancreatic trypsin inhibitor (BPTI) was one of the first to be elucidated and has served as a basis for understanding the folding pathways of other proteins. During the oxidative folding of reduced BPTI, two intermediates (N' and N*) accumulate in significant amounts and act as kinetic traps. Both N' and N* bury their two remaining free thiols in their hydrophobic cores, which inhibits further oxidation. Historically, the rate limiting step was considered to be the intramolecular rearrangements of N' and N* to another intermediate with two free thiols, N^{SH …}

Aspects Of The Innate Immune System In The Caribbean Octocoral Swiftia Exserta, Lorenzo P. Menzel

FIU Electronic Theses and Dissertations

The immune systems of cnidaria are important to study for two reasons: to gain a better understanding of the evolution of immune responses, and to provide a basis to partially redress the precipitous world-wide die-offs of reef corals, some of which have been attributed to diseases and stress. Many immune responses share ancient evolutionary origins and are common across many taxa.

Using Swiftia exserta, an azooxanthellate ahermatypic local octocoral, as a proxy model organism to study aspects of innate immunity in corals and cnidaria allows us to address both of the reasons listed above while not using endangered species. …

The Utilization Of Chiral Ion Mobility Spectrometry For The Detection Of Enantiomeric Mixtures And Thermally Labile Compounds, Howard K. Holness

FIU Electronic Theses and Dissertations

This dissertation utilized electrospray ion mobility mass spectrometry (ESI-IMS-MS) to develop methods necessary for the separation of chiral compounds of forensic interest. The compounds separated included ephedrines and pseudoephedrines, that occur as impurities in confiscated amphetamine type substances (ATS) in an effort to determine the origin of these substances. The ESI-IMS-MS technique proved to be faster and more cost effective than traditional chromatographic methods currently used to conduct chiral separations such as gas and liquid chromatography. Both mass spectrometric and computational analysis revealed the separation mechanism of these chiral interactions allowing for further development to separate other chiral compounds by …

Influence Of Soil Biogeochemical Properties On The Invasiveness Of Old World Climbing Fern (Lygodium Microphyllum), Pushpa Gautam Soti

FIU Electronic Theses and Dissertations

The state of Florida has one of the most severe exotic species invasion problems in the United States, but little is known about their influence on soil biogeochemistry. My dissertation research includes a cross-continental field study in Australia, Florida, and greenhouse and growth chamber experiments, focused on the soil-plant interactions of one of the most problematic weeds introduced in south Florida, Lygodium microphyllum (Old World climbing fern). Analysis of field samples from the ferns introduced and their native range indicate that L microphyllum is highly dependent on arbuscular mycorrhizal fungi (AMF) for phosphorus uptake and biomass accumulation. Relationship with AMF …

Regulation Of Rab5 Gtpase Activity During Pseudomonas Aeruginosa-Macrophage Interaction, Sushmita Mustafi

FIU Electronic Theses and Dissertations

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen. Several antibiotic resistant strains of P. aeruginosa are commonly found as secondary infection in immune-compromised patients leaving significant mortality and healthcare cost. Pseudomonas aeruginosa successfully avoids the process of phagocytosis, the first line of host defense, by secreting several toxic effectors. Effectors produced from P. aeruginosa Type III secretion system are critical molecules required to disrupt mammalian cell signaling and holds particular interest to the scientists studying host-pathogen interaction. Exoenzyme S (ExoS) is a bi-functional Type III effector that ADP-ribosylates several intracellular Ras (Rat sarcoma) and Rab (Response to abscisic acid) small GTPases …

Comprehensive Forensic Toxicological Analysis Of Designer Drugs, Madeleine Jean Swortwood

FIU Electronic Theses and Dissertations

New designer drugs are constantly emerging onto the illicit drug market and it is often difficult to validate and maintain comprehensive analytical methods for accurate detection of these compounds. Generally, toxicology laboratories utilize a screening method, such as immunoassay, for the presumptive identification of drugs of abuse. When a positive result occurs, confirmatory methods, such as gas chromatography (GC) or liquid chromatography (LC) coupled with mass spectrometry (MS), are required for more sensitive and specific analyses. In recent years, the need to study the activities of these compounds in screening assays as well as to develop confirmatory techniques to detect …

The Effect Of Contemporary Hydrologic Modification On Vegetation Community Composition Distinctness In The Florida Everglades, Ewan Isherwood

FIU Electronic Theses and Dissertations

The historic Everglades Ridge and Slough landscape maintained regularly spaced and elevated sawgrass ridges interspersed among exposed deeper-water sloughs; however, widespread but irregular hydrologic modification has degraded much of this landscape patterning. My study assessed the effects of hydrologic modification on vegetation community distinctness within the Ridge and Slough landscape through sampling species composition at fine-scales along a hydrologic gradient to measure the magnitude of segregation of species among patch types. The results show that vegetation community and topographic variation degradation is widespread, with distinctness differences proceeding and possibly being driven by topographic variation loss. Vegetation responses to past hydrologic …

Acclimatization Of The Tropical Reef Coral Acropora Millepora To Hyperthermal Stress, Anthony John Bellantuono

FIU Electronic Theses and Dissertations

The demise of reef-building corals potentially lies on the horizon, given ongoing climate change amid other anthropogenic environmental stressors. If corals cannot acclimatize or adapt to changing conditions, dramatic declines in the extent and health of the living reefs are expected within the next half century. The primary and proximal global threat to corals is climate change. Reef-building corals are dependent upon a nutritional symbiosis with photosynthetic dinoflagellates belonging to the group Symbiodinium. The symbiosis between the cnidarian host and algal partner is a stress-sensitive relationship; temperatures just 1°C above normal thermal maxima can result in the breakdown of …

Intraspecific Relationships In Paracalanus Quasimodo [Calinoideae] And Temora Turbinata [Calinoideae] Along The Southeastern Coast Of The United States, Richard Y. Chang

FIU Electronic Theses and Dissertations

Paracalanus quasimodo and Temora turbinata are two calanoid copepods prominent in the planktonic communities of the southeastern United States. Despite their prominence, the species and population level structure of these copepods is yet unexplored. The phylogeographic, temporal and phylogenetic structure of P. quasimodo and T. turbinata are examined in my study. Samples were collected from ten sites along the Gulf of Mexico and Florida peninsular coasts. Three sites were sampled quarterly for two years. Individuals were screened for unique ITS-1 sequences with denaturing gradient gel electrophoresis. Unique variants were sequenced at the nuclear ITS-1 and mitochondrial COI loci. Sampling sites …

Genetic Structure Of The Florida Key Tree Cactus, Pilosocereus Robinii, Using Restriction Site Associated Dna (Rad) Markers, Tonya D. Fotinos

FIU Electronic Theses and Dissertations

Rare plant conservation efforts must utilize current genetic methods to ensure the evolutionary potential of populations is preserved. One such effort involves the Key Tree Cactus, Pilosocereus robinii, which is an endangered columnar cactus native to the Florida Keys. The populations have precipitously declined over the past decade because of habitat loss and increasing soil salinity from rising sea levels and storm surge. Next-generation DNA sequencing was used to assess the genetic structure of the populations. Twenty individuals representative of both wild and extirpated cacti were chosen for Restriction Site Associated DNA (RAD) analysis. Samples processed using the HindIII …

Examining Gradients In Novelty: Native And Non-Native Fish Assemblages In Everglades Canals, David A. Gandy

FIU Electronic Theses and Dissertations

Novel ecosystems emerge from alterations to historic abiotic regimes and contain new species combinations. Everglades canals offer an opportunity to understand the function of novel habitat for native and non-native fishes and how novel conditions in turn influence distribution, abundance and assembly patterns. I examined native and non-native fish assemblages collected across a gradient in novelty, defined by the loss of wetland connectivity and habitat complexity. As novelty increased, native species richness and abundance strongly declined, and the contribution of non-natives increased. Community structure vastly differed among canals and was strongly influenced by spatial factors and secondarily by hydrological factors. …

Magnetic Nanoparticle-Based Targeted Drug Delivery For Treatment Of Neuro-Aids And Drug Addiction, Vidya Sagar

FIU Electronic Theses and Dissertations

Brain is one of the safe sanctuaries for HIV and, in turn, continuously supplies active viruses to the periphery. Additionally, HIV infection in brain results in several mild-to-severe neuro-immunological complications termed neuroAIDS. One-tenth of HIV-infected population is addicted to recreational drugs such as opiates, alcohol, nicotine, marijuana, etc. which share common target-areas in the brain with HIV. Interestingly, intensity of neuropathogenesis is remarkably enhanced due to exposure of recreational drugs during HIV infection. Current treatments to alleviate either the individual or synergistic effects of abusive drugs and HIV on neuronal modulations are less effective at CNS level, basically due to …

The Effects Of Arbuscular Mycorrhizal Fungi On Four Legume Hosts In South Florida Pine Rockland Soils, Klara Scharnagl

FIU Electronic Theses and Dissertations

This study addressed the effects of salinity and pot size on the interaction between leguminous plant hosts and arbuscular mycorrhizal fungi in four pine rockland soils using a shade house trap-plant experiment. Little is known about the belowground diversity of pine rocklands and the interactions between aboveground and belowground biota – an increased understanding of these interactions could lead to improved land management decisions, conservation and restoration efforts. Following twelve weeks of growth, plants were measured for root and shoot dry biomass and percent colonization by arbuscular mycorrhizal fungi. Overall, arbuscular mycorrhizal fungi had positive fitness effects on the four …

Wildfire Assessment Using Farsite Fire Modeling: A Case Study In The Chihuahua Desert Of Mexico, John Brakeall

FIU Electronic Theses and Dissertations

The Chihuahua desert is one of the most biologically diverse ecosystems in the world, but suffers serious degradation because of changes in fire regimes resulting in large catastrophic fires. My study was conducted in the Sierra La Mojonera (SLM) natural protected area in Mexico. The purpose of this study was to implement the use of FARSITE fire modeling as a fire management tool to develop an integrated fire management plan at SLM.

Firebreaks proved to detain 100% of wildfire outbreaks. The rosetophilous scrub experienced the fastest rate of fire spread and lowland creosote bush scrub experienced the slowest rate of …

Buckwheat As A Cover Crop In Florida: Mycorrhizal Status, Soil Analysis, And Economic Assessment, Daria Boglaienko

FIU Electronic Theses and Dissertations

This thesis analyses buckwheat as a cover crop in Florida. The study was designed to demonstrate: soil enrichment with nutrients, mycorrhizal arbuscular fungi interactions, growth in different soil types, temperature limitations in Florida, and economic benefits for farmers. Buckwheat was planted at the FIU organic garden (Miami, FL) in early November and harvested in middle December. After incorporation of buckwheat residues, soil analyses indicated the ability of buckwheat to enrich soil with major nutrients, in particular, phosphorus. Symbiosis with arbuscular mycorrhizal fungi increased inorganic phosphorus uptake and plant growth. Regression analysis on aboveground buckwheat biomass weight and soil characteristics showed …

The Role Of Teleost Grazers In A Relatively Pristine Seagrass Ecosystem, Cindy Bessey

FIU Electronic Theses and Dissertations

Trophic downgrading of ecosystems necessitates a functional understanding of trophic cascades. Identifying the presence of cascades, and the mechanisms through which they occur, is particularly important for seagrass meadows, which are among the most threatened ecosystems on Earth. Shark Bay, Western Australia provides a model system to investigate the potential importance of top-down effects in a relatively pristine seagrass ecosystem. The role of megagrazers in the Shark Bay system has been previously investigated, but the role of macrograzers (i.e., teleosts), and their importance relative to megagrazers, remains unknown. The objective of my dissertation was to elucidate the importance of teleost …

Effect Of The Supplemental Nutrition Assistance Program (Snap) And Nutrition Education On Nutrition And Health Outcomes Of Hiv+ Individuals, Irene Hatsu

FIU Electronic Theses and Dissertations

Factors associated with and barriers to participation in Supplemental Nutrition Assistance Program (SNAP) and the effect participation has on food security, nutrition status, disease status and quality of life was investigated in a cross-sectional study including 175 HIV infected individuals. In addition, the effect of a targeted nutrition education on nutrition knowledge, readiness to dietary behavior change, nutrition status, disease status and quality of life was also investigated among a subset of the population (N = 45) in a randomized clinical control trial.

SNAP participation rate was 70.3%, similar to the State of Florida and national participation rates. SNAP participation …

Factors Influencing Movements And Foraging Ecology Of American Alligators (Alligator Mississippiensis) In A Dynamic Subtropical Coastal Ecosystem, Adam Rosenblatt

FIU Electronic Theses and Dissertations

Top predators can have large effects on community and population dynamics but we still know relatively little about their roles in ecosystems and which biotic and abiotic factors potentially affect their behavioral patterns. Understanding the roles played by top predators is a pressing issue because many top predator populations around the world are declining rapidly yet we do not fully understand what the consequences of their potential extirpation could be for ecosystem structure and function. In addition, individual behavioral specialization is commonplace across many taxa, but studies of its prevalence, causes, and consequences in top predator populations are lacking. In …

Effects Of Multiple Ecological Drivers On Recruitment And Succession Of Coral Reef Macroalgal Communities, Alain Duran

FIU Electronic Theses and Dissertations

The study evaluated the effects of herbivory pressure, nutrient availability and potential propagule supply on recruitment and succession of coral reef macroalgal communities. Recruitment and succession tiles were placed in a nutrient-herbivory factorial experiment and macroalgal abundances were evaluated through time. Proportional abundances of macroalgal form-functional groups on recruitment and succession tiles were similar to field established communities within treatments, evidencing possible effects of adult macroalgae as propagule supply. Macroalgal abundance of recruitment tiles increased with nutrient loading and herbivory reduction combined whereas on succession tiles nutrient loading increased abundance of articulated-calcareous only when herbivores were excluded. Macroalgal field established …

Aedes Aegypti Pharate First Instar Aseasonal Quiescence Cues Anticipatory Plasticity With Implications For Urban Vector Ecology And Control, Mario H. Perez

FIU Electronic Theses and Dissertations

The eggs of the dengue fever vector Aedes aegypti possess the ability to undergo an extended quiescence period hosting a fully developed first instar larvae within its chorion. As a result of this life history stage, pharate larvae can withstand months of dormancy inside the egg where they depend on stored reserves of maternal origin. This adaptation known as pharate first instar quiescence, allows A. aegypti to cope with fluctuations in water availability. An examination of this fundamental adaptation has shown that there are trade-offs associated with it.

Aedes aegypti mosquitoes are frequently associated with urban habitats that may contain …

Root:Shoot Ratio And Specific Leaf Area Along An Elevational Gradient In The Peruvian Andes, Catherine Heidy Bravo Avila

FIU Electronic Theses and Dissertations

Andean montane forests are one of the most diverse ecosystems on Earth, but are also highly vulnerable to climate change. Therefore, the link between plant distribution and ecosystem productivity is a critical point to investigate in these ecosystems. Are the patterns in productivity observed in montane forest due to species turnover along the elevational gradients? Methodological constraints keep this question unanswered. Also, despite their importance, belowground biomass remains poorly quantified and understood. I measured two plant functional traits in seedlings, root:shoot ratio and specific leaf area, to identify different strategies in growth and biomass allocation across elevations. A tradeoff in …

Multifunctional Nanoparticles In Cancer: In Vitro Characterization, In Vivo Distribution, Tingjun Lei

FIU Electronic Theses and Dissertations

A novel biocompatible and biodegradable polymer, termed poly(Glycerol malate co-dodecanedioate) (PGMD), was prepared by thermal condensation method and used for fabrication of nanoparticles (NPs). PGMD NPs were prepared using the single oil emulsion technique and loaded with an imaging/hyperthermia agent (IR820) and a chemotherapeutic agent (doxorubicin, DOX). The size of the void PGMD NPs, IR820-PGMD NPs and DOX-IR820-PGMD NPs were approximately 90 nm, 110 nm, and 125 nm respectively. An acidic environment (pH=5.0) induced higher DOX and IR820 release compared to pH=7.4. DOX release was also enhanced by exposure to laser, which increased the temperature to 42°C. Cytotoxicity of DOX-IR820-PGMD …

Pseudomonas Aeruginosa Ampr Transcriptional Regulatory Network, Deepak Balasubramanian

FIU Electronic Theses and Dissertations

In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion …

Nuclear Magnetic Resonance Spectroscopic And Computational Investigations Of Chloroperoxidase Catalyzed Regio- And Enantio-Selective Transformations, Rui Zhang

FIU Electronic Theses and Dissertations

Chloroperoxidase (CPO) is the most versatile heme-containing enzyme that catalyzes a broad spectrum of reactions. The remarkable feature of this enzyme is the high regio- and enantio-selectivity exhibited in CPO-catalyzed oxidation reactions. The aim of this dissertation is to elucidate the structural basis for regio- and enantio-selective transformations and investigate the application of CPO in biodegradation of synthetic dyes.

To unravel the mechanism of CPO-catalyzed regioselective oxidation of indole, the dissertation explored the structure of CPO-indole complex using paramagnetic relaxation and molecular modeling. The distances between the protons of indole and the heme iron revealed that the pyrrole ring of …

Does Landscape Context Affect Habitat Value? The Importance Of Seascape Ecology In Back-Reef Systems, Lauren Yeager

FIU Electronic Theses and Dissertations

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created …