Life Sciences Commons^™

Density Dependence Drives Habitat Production And Survivorship Of Acropora Cervicornis Used For Restoration On A Caribbean Coral Reef, Mark C. Ladd, Andrew A. Shantz, Ken Nedimyer, Deron E. Burkepile

Department of Biological Sciences

Coral restoration is gaining traction as a viable strategy to help restore degraded reefs. While the nascent field of coral restoration has rapidly progressed in the past decade, significant knowledge gaps remain regarding the drivers of restoration success that may impede our ability to effectively restore coral reef communities. Here, we conducted a field experiment to investigate the influence of coral density on the growth, habitat production, and survival of corals outplanted for restoration. We used nursery-raised colonies of Acropora cervicornis to experimentally establish populations of corals with either 3, 6, 12, or 24 corals within 4m² plots, generating …

Design And Synthesis Of Novel Azasteroids And Pseudoazulenyl Nitrones, Nagaraju Birudukota

FIU Electronic Theses and Dissertations

Steroids are one of the essential classes of bioactive compounds and are involved in many biological functions which include their role as signaling compounds, the alteration of membrane fluidity and the regulation of a variety of metabolic processes. In order to identify novel compounds with beneficial pharmacological action, the synthesis of modified steroids is gaining much attention in recent years. Among those analogs, azasteroids are one of the most important classes which display a variety of biological activities, often free from undesirable side effects. The challenges in the synthesis of steroids, particularly azasteroids, and the potential of azasteroids as novel …

Short-Term Dissolved Organic Carbon Dynamics Reflect Tidal, Water Management, And Precipitation Patterns In A Subtropical Estuary, Peter Regier, Rudolf Jaffe

Department of Chemistry and Biochemistry

Estuaries significantly impact the global carbon cycle by regulating the exchange of organic matter, primarily in the form of dissolved organic carbon (DOC), between terrestrial and marine carbon pools. Estuarine DOC dynamics are complex as tides and other hydrological and climatic drivers can affect carbon fluxes on short and long time scales. While estuarine and coastal DOC dynamics have been well-studied, variations on short time scales are less well-constrained. Recent advancements in sonde technology enable autonomous in situ collection of high frequency DOC data using fluorescent dissolved organic matter (FDOM) as a proxy, dramatically improving our capacity to characterize rapid …

Inferring Animal Social Networks And Leadership: Applications For Passive Monitoring Arrays, David M.P. Jacoby, Yannis Papastamatiou, Robin Freeman

Center for Coastal Oceans Research Faculty Publications

Analyses of animal social networks have frequently benefited from techniques derived from other disciplines. Recently, machine learning algorithms have been adopted to infer social associations from time-series data gathered using remote, telemetry systems situated at provisioning sites. We adapt and modify existing inference methods to reveal the underlying social structure of wide-ranging marine predators moving through spatial arrays of passive acoustic receivers. From six months of tracking data for grey reef sharks (Carcharhinus amblyrhynchos) at Palmyra atoll in the Pacific Ocean, we demonstrate that some individuals emerge as leaders within the population and that this behavioural coordination is …

Otopathogenic Pseudomonas Aeruginosa Enters And Survives Inside Macrophages, Rahul Mittal, Christopher V. Lisi, Hansi Kumari, M'Hamed Grati, Patricia Blackwelder, Denise Yan, Chaitanya Jain, Kalai Mathee, Paulo H. Weckwerth, Xue Z. Liu

Biomolecular Sciences Institute: Faculty Publications

Otitis media (OM) is a broad term describing a group of infectious and inflammatory disorders of the middle ear. Despite antibiotic therapy, acute OM can progress to chronic suppurative otitis media (CSOM) characterized by ear drum perforation and purulent discharge. Pseudomonas aeruginosa is the most common pathogen associated with CSOM. Although, macrophages play an important role in innate immune responses but their role in the pathogenesis of P. aeruginosa-induced CSOM is not known. The objective of this study is to examine the interaction of P. aeruginosa with primary macrophages. We observed that P. aeruginosa enters and multiplies inside human …

Avoiding Regions Symptomatic Of Conformational And Functional Flexibility To Identify Antiviral Targets In Current And Future Coronaviruses, Jordon Rahaman, Jessica Siltberg-Liberles

Biomolecular Sciences Institute: Faculty Publications

Within the last 15 years, two related coronaviruses (Severe Acute Respiratory Syndrome [SARS]-CoV and Middle East Respiratory Syndrome [MERS]-CoV) expanded their host range to include humans, with increased virulence in their new host. Coronaviruses were recently found to have little intrinsic disorder compared with many other virus families. Because intrinsically disordered regions have been proposed to be important for rewiring interactions between virus and host, we investigated the conservation of intrinsic disorder and secondary structure in coronaviruses in an evolutionary context. We found that regions of intrinsic disorder are rarely conserved among different coronavirus protein families, with the primary exception …

A Framework For Assessing Alternative Agro-Ecosystems: Finding Multi-Functional Solutions For Sustainable Urban Landscapes., Thais H. Thiesen Ms.

FIU Electronic Theses and Dissertations

Creating sustainable urban landscapes in light of growing population pressures requires interdisciplinary multi-functional solutions. Alternative agro-ecosystems described as food forests, permaculture gardens, and/or edible landscapes among others could offer potential ways to address the social, economic and ecological goals of various stakeholders simultaneously. The present research used a unique rubric, the Permaculture and Agro-ecosystems Sustainability Scorecard (PASS) that combines existing agricultural and landscape sustainability indicators in order to assess alternative agro-ecosystems. The rubric evaluates provisioning, regulating, supporting and cultural ecosystem services such as pollinator presence, biodiversity, pesticides and fertilizer use, carbon sequestration and human interactions. The PASS was used to …

Characterization Of Interaction Between Brevetoxin And Its Native Receptor And Identification Of The Role Of Brevetoxin In Karenia Brevis, Wei Chen

FIU Electronic Theses and Dissertations

Algae are important to marine and fresh-water ecosystems. However, some species of algae are harmful or even toxic. They can consume oxygen or block sunlight that is essential for other organisms to live. Indeed, some algae blooms can produce toxins that damage the health of the environment, plants, animals, and humans. Harmful algal blooms (HABs) which are often more green, brown, or dark-colored than red have spread along the coastlines and in the surface waters of the United States. Therefore, scientists are making great efforts to study HABs in order to maintain human and ecosystem health.

Karenia brevis, the …

Effects Of Catastrophic Seagrass Loss And Predation Risk On The Ecological Structure And Resilience Of A Model Seagrass Ecosystem, Robert J. Nowicki

FIU Electronic Theses and Dissertations

As climate change continues, climactic extremes are predicted to become more frequent and intense, in some cases resulting in dramatic changes to ecosystems. The effects of climate change on ecosystems will be mediated, in part, by biotic interactions in those ecosystems. However, there is still considerable uncertainty about where and how such biotic interactions will be important in the context of ecosystem disturbance and climactic extremes.

Here, I review the role of consumers in seagrass ecosystems and investigate the ecological impacts of an extreme climactic event (marine heat wave) and subsequent widespread seagrass die-off in Shark Bay, Western Australia. Specifically, …

An Ecological Study Of The Anurans In Tea Plantations In A Biodiversity Hotspot, Lilly M. Eluvathingal

FIU Electronic Theses and Dissertations

Increasing human population size is increasing the demand for resources like timber, oil, tea, coffee, and other crops. Plantation crops mimic some aspects of native habitats, and there are studies that report the presence of some native anuran biodiversity in plantations. I focused on tea plantations in the Western Ghats-Sri Lanka Biodiversity Hotspot and studied the diversity and health of anurans in different habitats found within a tea cultivation area, near Munnar region in the Western Ghats, India. The landscape includes tea bushes, native evergreen shola forest patches, and eucalyptus forest stands. I reviewed 40 studies comparing amphibian species richness …

Brain Networks Supporting Literacy Development, Iris J. Broce

FIU Electronic Theses and Dissertations

The development of fluent reading requires coordinated development of key fiber pathways. While several fiber pathways have been implicated in reading, including the recently re-identified vertical occipital fasciculus (VOF), inferior longitudinal fasciculus (ILF), arcuate fasciculus and its 3 components, and inferior fronto-occipital fasciculus (IFOF), whether these fiber pathways support reading in young children with little to no exposure to print remains poorly understood. Consequently, over the course of three studies, the current dissertation aimed to narrow this research gap by addressing the following research questions: 1) Which fiber pathways support early literacy skill in young children 5-10 years old? 2) …

Screening Of Plants For Antibacterial Properties: Growth Inhibition Of Staphylococcus Aureus By Artemisia Tridentata, Steven Ross Eichelbaum

FIU Electronic Theses and Dissertations

Drug-resistant pathogenic and opportunistic bacteria are increasing in occurrence and prevalence, and pose a dangerous threat to human health. In the search for novel antibiotics with which to combat this threat, plants, specifically those used in traditional medicine with ascribed antibacterial properties, offer a promising and potentially vast source of such therapeutic compounds. The purpose of this study was therefore to screen chemical extracts created from various plant species for antibacterial properties versus pathogenic bacterial species. In the course of these antibacterial assays, we successfully identified a methanol extract derived from Artemisia tridentata tridentata plant material as capable of inhibiting …

Targeted And Controlled Anticancer Drug Delivery And Release With Magnetoelectric Nanoparticles, Alexandra Rodzinski

FIU Electronic Theses and Dissertations

A major challenge of cancer treatment is successful discrimination of cancer cells from healthy cells. Nanotechnology offers multiple venues for efficient cancer targeting. Magnetoelectric nanoparticles (MENs) are a novel, multifaceted, physics-based cancer treatment platform that enables high specificity cancer targeting and externally controlled loaded drug release. The unique magnetoelectric coupling of MENs allows them to convert externally applied magnetic fields into intrinsic electric signals, which allows MENs to both be drawn magnetically towards the cancer site and to electrically interface with cancer cells. Once internalized, the MEN payload release can be externally triggered with a magnetic field. MENs uniquely allow …

The Optimization Of Pressure Cycling Technology (Pct) For Differential Extraction Of Sexual Assault Casework, Vanessa Martinez

FIU Electronic Theses and Dissertations

A two-step protocol has been devised as a rapid and selective alternative to conventional differential extraction techniques with an increased recovery of DNA. The protocol involves pressure cycling with the Barocycler^® NEP 2320 from Pressure Biosciences. Inc. in alkaline conditions for epithelial cell lysis and removal. This step is followed by alkaline lysis at 95^º C for extraction of sperm cell DNA. At 1:1 or 2:1 female to male cell ratios, high selectivity and complete separation can be achieved. But at higher ratios, male allelic dropout is observed. This protocol has been modified to generate a clean male …

Elucidating The Role Of Mifs-Mifr Two-Component System In Regulating Pseudomonas Aeruginosa Pathogenicity, Gorakh Digambar Tatke

FIU Electronic Theses and Dissertations

Pseudomonas aeruginosa is a Gram-negative, metabolically versatile, opportunistic pathogen that exhibits a multitude of virulence factors, and is extraordinarily resistant to a gamut of clinically significant antibiotics. This ability is in part mediated by two-component systems (TCS) that play a crucial role in regulating virulence mechanisms, metabolism and antibiotic resistance. Our sequence analysis of the P. aeruginosa PAO1 genome revealed the presence of two open reading frames, mifS and mifR, which encodes putative TCS proteins, a histidine sensor kinase MifS and a response regulator MifR, respectively. This two-gene operon was found immediately upstream of the poxAB operon, where poxB encodes …

Seasonal Regulation Of Herbivory And Nutrient Effects On Macroalgal Recruitment And Succession In A Florida Coral Reef, Alain Duran, Ligia Collado-Vides, Deron E. Burkepile

Department of Biological Sciences

Herbivory and nutrient enrichment are drivers of benthic dynamics of coral reef macroalgae; however, their impact may vary seasonally. In this study we evaluated the effects of herbivore pressure, nutrient availability and potential propagule supply on seasonal recruitment and succession of macroalgal communities on a Florida coral reef. Recruitment tiles, replaced every three months, and succession tiles, kept in the field for nine months, were established in an ongoing factorial nutrient enrichment-herbivore exclusion experiment. The ongoing experiment had already created very different algal communities across the different herbivory and nutrient treatments. We tracked algal recruitment, species richness, and species abundance …

Microbial Functional Diversity And The Associated Biogeochemical Interactions Across Miami-Dade County, Florida Soils, Priyanka Kushwaha

FIU Electronic Theses and Dissertations

Decomposition of soil organic matter by microbial processes results in carbon sequestration within soils and/or carbon loss via atmospheric emission of carbon dioxide and methane. Natural as well as anthropogenic factors have been documented to impact soil microbial diversity and the associated biogeochemical functions. The soil microbial communities co-inhabiting Miami-Dade County soils, Florida are under threat because of the ongoing restoration efforts in the adjoining Florida Everglades Parks, predicted climatic changes such as sea-level rise and high rainfall, as well as urbanization. Therefore, an improved understanding of the current microbial functional communities is essential to better assess the impact of …

Fluorescently Labeled Circular Dna Molecules For Dna Topology And Topoisomerases, Maxwell Gu, Andrea Berrido, Walter Gonzalez, Jaroslava Miksovska, Jeremy W. Chambers, Fenfei Leng

Biomolecular Sciences Institute: Faculty Publications

DNA topology plays essential roles in several fundamental biological processes, such as DNA replication, recombination, and transcription. Typically agarose gel electrophoresis is employed to study DNA topology. Since gel electrophoresis is time-consuming and labor intensive, it is desirable to develop other methods, such as fluorescence-based methods, for such studies. In this paper we report the synthesis of a type of unique fluorescence-labeled DNA molecules that can be used to study DNA topology and topoisomerases by fluorescence resonance energy transfer (FRET). Specifically, we inserted an 82 nt. synthetic DNA oligomer FL905 carrying a 42 nt. AT sequence with fluorescein and dabcyl …

Phylogeny Of Stenopodidea (Crustacea: Decapoda) Shrimps Inferred From Nuclear And Mitochondrial Genes Reveals Non-Monophyly Of The Families Spongicolidae And Stenopididae, And Most Of Their Composite Genera, Chien-Lin Chen, Joseph W. Goy, Heather D. Bracken-Grissom, Darryl L. Felder, Ling Ming Tsang, Tin-Yam Chan

Center for Coastal Oceans Research Faculty Publications

The infraorder Stenopodidea is a relatively small group of marine decapod crustaceans including the well known cleaner shrimps, but their higher taxonomy has been rather controversial. This study provides the most comprehensive molecular phylogenetic analyses of Stenopodidea using sequence data from two mitochondrial (16S and 12S rRNA) and two nuclear (histone H3 and sodium–potassium ATPase α-subunit (NaK)) genes. We included all 12 nominal genera from the three stenopodidean families in order to test the proposed evolutionary hypothesis and taxonomic scheme of the group. The inferred phylogeny did not support the familial ranking of Macromaxillocarididae and rejected the reciprocal monophyly of …

Biogeographical Patterns Of Soil Microbial Communities: Ecological, Structural, And Functional Diversity And Their Application To Soil Provenance, Natalie Damaso

FIU Electronic Theses and Dissertations

The current ecological hypothesis states that the soil type (e.g., chemical and physical properties) determines which microbes occupy a particular soil and provides the foundation for soil provenance studies. As human profiles are used to determine a match between evidence from a crime scene and a suspect, a soil microbial profile can be used to determine a match between soil found on the suspect’s shoes or clothing to the soil at a crime scene. However, for a robust tool to be applied in forensic application, an understanding of the uncertainty associated with any comparisons and the parameters that can significantly …

Relations Between Morphology, Buoyancy And Energetics Of Requiem Sharks, Gil Iosilevskii, Yannis Papastamatiou

Center for Coastal Oceans Research Faculty Publications

Sharks have a distinctive shape that remained practically unchanged through hundreds of millions of years of evolution. Nonetheless, there are variations of this shape that vary between and within species. We attempt to explain these variations by examining the partial derivatives of the cost of transport of a generic shark with respect to buoyancy, span and chord of its pectoral fins, length, girth and body temperature. Our analysis predicts an intricate relation between these parameters, suggesting that ectothermic species residing in cooler temperatures must either have longer pectoral fins and/or be more buoyant in order to maintain swimming performance. It …

A Morphological, Functional, And Genetic Investigation Of The Male Compound Eye Phenotype Of Chrysomya Megacephala (Diptera: Calliphoridae)), Joshua Smith

FIU Electronic Theses and Dissertations

A very unique compound eye in dipterans is found in males of the forensically important blow fly, Chrysomya megacephala (Diptera: Calliphoridae). This compound eye is characterized by an area of enlarged dorsal facets that, unlike almost all other regional changes in dipteran ommatidia size, is not accompanied by a change in resolution. This region is believed to play a role in mate tracking and allow for increased light capture, though no behavioral studies have tested these claims. An initial goal of the dissertation was to examine the function of this compound eye. Using allometric measurements coupled with behavioral tests, I …

Trace Element And Isotope Deposition Across The Air–Sea Interface: Progress And Research Needs, A. R. Baker, W. M. Landing, E. Bucciarelli, S. Fietz, C. T. Hayes, David C. Kadko, P. L. Morton, N. Rogan, G. Sarthou, R. U. Shelley, Z. Shi, A. Shiller, M.M. P. Van Hulten

Center for Coastal Oceans Research Faculty Publications

The importance of the atmospheric deposition of biologically essential trace elements, especially iron, is widely recognized, as are the difficulties of accurately quantifying the rates of trace element wet and dry deposition and their fractional solubility. This paper summarizes some of the recent progress in this field, particularly that driven by the GEOTRACES, and other, international research programmes. The utility and limitations of models used to estimate atmospheric deposition flux, for example, from the surface ocean distribution of tracers such as dissolved aluminium, are discussed and a relatively new technique for quantifying atmospheric deposition using the short-lived radionuclide beryllium-7 is …

A Review Of Subtropical Community Resistance And Resilience To Extreme Cold Spells, Ross E. Boucek, Evelyn E. Gaiser, H. Liu, Jennifer S. Rehage

FCE LTER Journal Articles

Forecasted changes in global climate predict not only shifts in average conditions but also changes in the frequency and intensity of climate extremes. In the subtropics, the passage of extreme cold spells functions as a major structuring force for ecological communities, and can incur substantial losses to biodiversity, agriculture, and infrastructure. If these events persist in the future, it is likely that their effects on subtropical communities and ecosystems will become more pronounced, as tropical species migrate poleward. Recent extreme cold spells in subtropical China (2008) and United States (2010) occurred in ecosystems that are the subject of long-term ecological …

Profiling Populations Using Neutral Markers, Major Histocompatibility Complex Genes And Volatile Organic Compounds As Modeled In Equus Caballus Linnaeus, Ketaki Deshpande

FIU Electronic Theses and Dissertations

Assessing the genetics of wild animal populations aims to understand selective pressures, and factors whether it be inbreeding or adaptation, that affect the genome. Although numerous techniques are available for assessing population structure, a major obstacle in studying wild populations is obtaining samples from the animals without having to capture them, which can lead to undue distress and injury. Therefore, biologists often use non-invasive sampling methods (i.e., collection of feces, hair) to extract host DNA. In this study, new DNA extraction protocols were developed that improved the quality and quantity of DNA obtained from fecal matter. Fecal samples aged up …

Environmental Drivers Of Diurnal Visits By Transient Predatory Fishes To Caribbean Patch Reefs, Alastair R. Harbonne, J. D. Selwyn, J. M. Lawson, M. Galo

Center for Coastal Oceans Research Faculty Publications

Video cameras recorded the diurnal visitation rates of transient (large home range) piscivorous fishes to coral patch reefs in The Bahamas and identified 11 species. Visits by bar jack Caranx ruber, mutton snapper Lutjanus analis, yellowtail snapper Ocyurus chrysurus, barracuda Sphyraena barracuda and cero Scomberomorus regalis were sufficiently frequent to correlate with a range of biophysical factors. Patch-reef visitation rates and fish abundances varied with distance from shore and all species except S. regalis were seen more frequently inshore. This pattern is likely to be caused by factors including close proximity to additional foraging areas in mangroves …

Fce Iii Year Four Annual Report For Nsf Award Dbe- 1237517 (2016), Evelyn E. Gaiser, Michael R. Heithaus, Rudolf Jaffe, John Kominoski, René M. Price

FCE - LTER Annual Reports and Proposals

No abstract provided.

Trinucleotide Repeat Instability Is Modulated By Dna Base Lesions And Dna Base Excision Repair, Jill M. Beaver

FIU Electronic Theses and Dissertations

Trinucleotide repeat (TNR) expansions are the cause of over 40 human neurodegenerative diseases, and are linked to DNA damage and base excision repair (BER). We explored the role of DNA damage and BER in modulating TNR instability through analysis of DNA structures, BER protein activities, and reconstitution of repair using human BER proteins and synthesized DNA containing various types of damage. We show that DNA damage and BER can modulate TNR expansions by promoting removal of a TNR hairpin through coordinated activities of BER proteins and cofactors. We found that during repair in a TNR hairpin, coordination between the 5’-flap …

Uniting Paradigms Of Connectivity In Marine Ecology, Christopher J. Brown, Alastair R. Harborne, Claire B. Paris, Peter J. Mumby

Center for Coastal Oceans Research Faculty Publications

The connectivity of marine organisms among habitat patches has been dominated by two independent paradigms with distinct conservation strategies. One paradigm is the dispersal of larvae on ocean currents, which suggests networks of marine reserves. The other is the demersal migration of animals from nursery to adult habitats, requiring the conservation of connected ecosystem corridors. Here, we suggest that a common driver, wave exposure, links larval and demersal connectivity across the seascape. To study the effect of linked connectivities on fish abundance at reefs, we parameterize a demographic model for The Bahamas seascape using maps of habitats, empirically forced models …

Investigating Sub-Tropical Community Resistance And Resilience To Climate Disturbance, Ross E. Boucek

FIU Electronic Theses and Dissertations

Changes in global climate will likely increase climate variability. In turn, changes in climate variability have begun to alter the frequency, intensity, and timing of climate disturbances. Continued changes in the climate disturbance regime experienced by natural systems will undoubtedly affect ecological processes at every hierarchical scale. Thus, in order to predict the dynamics of ecological systems in the future, we must develop a more mechanistic understanding of how and in what ways climate disturbance affects natural systems. In South Florida, two climate disturbances recently affected the region, a severe cold spell in 2010, and a drought in 2011. Importantly, …