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- Title
- MESSENGER RNA PROFILING: A PROTOTYPE METHOD FOR BODY FLUIDAND TISSUE IDENTIFICATION.
- Creator
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Juusola, Jane, Ballantyne, Jack, University of Central Florida
- Abstract / Description
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Conventional methods of body fluid identification use labor-intensive, technologically diverse techniques that are performed in a series, not parallel, manner and are costly in terms of time and sample. Furthermore, for some frequently encountered body fluids, such as saliva or vaginal secretions, no confirmatory technique exists. Terminally differentiated cells, such as blood lymphocytes or epithelial cells lining the oral cavity, have a unique pattern of gene expression, which is evinced by...
Show moreConventional methods of body fluid identification use labor-intensive, technologically diverse techniques that are performed in a series, not parallel, manner and are costly in terms of time and sample. Furthermore, for some frequently encountered body fluids, such as saliva or vaginal secretions, no confirmatory technique exists. Terminally differentiated cells, such as blood lymphocytes or epithelial cells lining the oral cavity, have a unique pattern of gene expression, which is evinced by the presence and relative abundance of specific mRNA species. If the type and abundance of mRNAs can be determined in a stain or tissue sample recovered at the crime scene, it would be possible to definitively identify the tissue or body fluid in question. Advantages of an mRNA-based approach, compared to conventional biochemical analysis, include greater specificity, simultaneous and semi-automated analysis though a common assay format, improved timeliness, decreased sample consumption and compatibility with DNA extraction methodologies. In this report, we demonstrate that RNA is stable in biological stains and can be recovered in sufficient quantity and quality for analysis using reverse transcriptasepolymerase chain reaction assay (RT-PCR). We have identified sets of candidate tissuespecific genes for body fluids and tissues of forensic interest, namely blood, saliva, semen, vaginal secretions, menstrual blood, urine, skin, muscle, adipose, and brain. We also report the identification of a new housekeeping gene for use in mRNA based assays. Select body fluid-specific genes have been incorporated into multiplex PCR and real-time PCR assays. These assays allow for the positive identification of blood, saliva, semen,vaginal secretions, and/or menstrual blood in a stain. The final task of this work was the molecular characterization of mRNA degradation patterns in biological stains, which not only has fundamental importance in possibly revealing mRNA degradation pathways in dried biological stains, but may ultimately lead to better assay design strategies for mRNA markers for forensic use. An mRNA-based approach described in this report could allow the facile identification of the tissue components present in a body fluid stain and could conceivably supplant the battery of serological and biochemical tests currently employed in the forensic serology laboratory.
Show less - Date Issued
- 2005
- Identifier
- CFE0000862, ucf:46668
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0000862
- Title
- Application of Landfill Treatment Approaches for the Stabilization of Municipal Solid Waste.
- Creator
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Bolyard, Stephanie, Reinhart, Debra, Santra, Swadeshmukul, Randall, Andrew, University of Central Florida
- Abstract / Description
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This research focused on the fundamental requirements of stabilizing a mature landfill using three treatment approaches as well as the implications of discharging leachate organic matter (LOM) to wastewater treatment plants (WWTPs). Three treatment approaches aimed at removing releasable carbon and nitrogen from mature landfills including flushing with clean water, leachate recirculation with ex-situ chemical oxidation, and leachate recirculation with ex-situ chemical oxidation and in-situ...
Show moreThis research focused on the fundamental requirements of stabilizing a mature landfill using three treatment approaches as well as the implications of discharging leachate organic matter (LOM) to wastewater treatment plants (WWTPs). Three treatment approaches aimed at removing releasable carbon and nitrogen from mature landfills including flushing with clean water, leachate recirculation with ex-situ chemical oxidation, and leachate recirculation with ex-situ chemical oxidation and in-situ aeration were evaluated. After extensive treatment of the waste in the flushing bioreactor (FB) scenarios, the overall biodegradable fraction was reduced relative to mature waste. Leachate quality improved for all FBs but through different mechanisms. Flushing was the most effective approach at removing biodegradable components and improving leachate quality. A mass balance on carbon and nitrogen revealed that a significant fraction still remained in the waste. Solid waste and leachate samples from the anaerobic bioreactors and FBs were characterized using Fourier Transform Infrared (FTIR) to provide a better understanding of changes in waste characteristics when waste transitions from mature to stabilized. Organic functional groups associated with aliphatic methylene were present in leachate and solid waste samples during the early stages of anaerobic degradation and disappeared once these wastes underwent treatment. Once the waste was stabilized, the FTIR spectra of leachate and solid waste were dominated by inorganic functional groups (carboxylic acid/carbonate group, carbonate, quartz, and clay minerals). Leachate is commonly co-treated with domestic wastewater due to the cost and complexity of on-site treatment. The organic constituents in leachate can be problematic for WWTPs as their recalcitrant components pass through conventional treatment processes, impacting effluent quality. Twelve leachates where characterized for total nitrogen (TN) and dissolved organic nitrogen (DON). The average concentration of TN and DON in leachate was 1,160 and 40.7 mg/L, respectively. Leachates were fractionated based on hydrophobic (recalcitrant; rDON) and hydrophilic (bioavailable; bDON) properties. The average concentrations of bDON and rDON were 16.5 and 18.4 mg/L, respectively. Multiple leachate and wastewater co-treatment simulations were carried out to assess the treatment of leachate nitrogen at historic nitrogen removal levels of four WWTPs and the effects on wastewater effluent quality for four WWTPs. The effluent quality exceeded typical TN limits of 3 to 10 mg/L at leachate volumetric contributions of 10%. The maximum calculated pass through concentrations of rDON and DON at 10% volumetric contribution for the twelve leachates was 4.77 and 9.71 mg/L, respectively. The effects of LOM on wastewater effluent quality was further evaluated in the field. Results showed that leachate detection for each field study could be determined using UV254 nm absorbance. DON and dissolved organic carbon (DOC) concentrations increased at significant levels in leachate-impacted wastewater samples. The DON decreased through the treatment train, suggesting that this parameter was effectively removed, while DOC persisted. DOC pass through coincided with an increase in color and UV254 nm absorption. In effluents, the UV254 nm transmittance was just below the minimum 65% disinfection requirement at dilutions greater than 1%. Leachate-impacted wastewater showed a higher concentration of humic-like peaks during fluorescence measurements than wastewater without leachate.
Show less - Date Issued
- 2016
- Identifier
- CFE0006076, ucf:50959
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006076
- Title
- Stability and Control in Complex Networks of Dynamical Systems.
- Creator
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Manaffam, Saeed, Vosoughi, Azadeh, Behal, Aman, Atia, George, Rahnavard, Nazanin, Javidi, Tara, Das, Tuhin, University of Central Florida
- Abstract / Description
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Stability analysis of networked dynamical systems has been of interest in many disciplines such as biology and physics and chemistry with applications such as LASER cooling and plasma stability. These large networks are often modeled to have a completely random (Erd\"os-R\'enyi) or semi-random (Small-World) topologies. The former model is often used due to mathematical tractability while the latter has been shown to be a better model for most real life networks.The recent emergence of cyber...
Show moreStability analysis of networked dynamical systems has been of interest in many disciplines such as biology and physics and chemistry with applications such as LASER cooling and plasma stability. These large networks are often modeled to have a completely random (Erd\"os-R\'enyi) or semi-random (Small-World) topologies. The former model is often used due to mathematical tractability while the latter has been shown to be a better model for most real life networks.The recent emergence of cyber physical systems, and in particular the smart grid, has given rise to a number of engineering questions regarding the control and optimization of such networks. Some of the these questions are: \emph{How can the stability of a random network be characterized in probabilistic terms? Can the effects of network topology and system dynamics be separated? What does it take to control a large random network? Can decentralized (pinning) control be effective? If not, how large does the control network needs to be? How can decentralized or distributed controllers be designed? How the size of control network would scale with the size of networked system?}Motivated by these questions, we began by studying the probability of stability of synchronization in random networks of oscillators. We developed a stability condition separating the effects of topology and node dynamics and evaluated bounds on the probability of stability for both Erd\"os-R\'enyi (ER) and Small-World (SW) network topology models. We then turned our attention to the more realistic scenario where the dynamics of the nodes and couplings are mismatched. Utilizing the concept of $\varepsilon$-synchronization, we have studied the probability of synchronization and showed that the synchronization error, $\varepsilon$, can be arbitrarily reduced using linear controllers.We have also considered the decentralized approach of pinning control to ensure stability in such complex networks. In the pinning method, decentralized controllers are used to control a fraction of the nodes in the network. This is different from traditional decentralized approaches where all the nodes have their own controllers. While the problem of selecting the minimum number of pinning nodes is known to be NP-hard and grows exponentially with the number of nodes in the network we have devised a suboptimal algorithm to select the pinning nodes which converges linearly with network size. We have also analyzed the effectiveness of the pinning approach for the synchronization of oscillators in the networks with fast switching, where the network links disconnect and reconnect quickly relative to the node dynamics.To address the scaling problem in the design of distributed control networks, we have employed a random control network to stabilize a random plant network. Our results show that for an ER plant network, the control network needs to grow linearly with the size of the plant network.
Show less - Date Issued
- 2015
- Identifier
- CFE0005834, ucf:50902
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005834
- Title
- computational study of traveling wave solutions and global stability of predator-prey models.
- Creator
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Zhu, Yi, Qi, Yuanwei, Rollins, David, Shuai, Zhisheng, Zhai, Lei, University of Central Florida
- Abstract / Description
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In this thesis, we study two types of reaction-diffusion systems which have direct applications in understanding wide range of phenomena in chemical reaction, biological pattern formation and theoretical ecology.The first part of this thesis is on propagating traveling waves in a class of reaction-diffusion systems which model isothermal autocatalytic chemical reactions as well as microbial growth and competition in a flow reactor. In the context of isothermal autocatalytic systems, two...
Show moreIn this thesis, we study two types of reaction-diffusion systems which have direct applications in understanding wide range of phenomena in chemical reaction, biological pattern formation and theoretical ecology.The first part of this thesis is on propagating traveling waves in a class of reaction-diffusion systems which model isothermal autocatalytic chemical reactions as well as microbial growth and competition in a flow reactor. In the context of isothermal autocatalytic systems, two different cases will bestudied. The first is autocatalytic chemical reaction of order $m$ without decay. The second is chemical reaction of order $m$ with a decay of order $l$, where $m$ and $l$ are positive integers and $m(>)l\ge1$. A typical system is $A + 2B \rightarrow3B$ and $B\rightarrow C$ involving three chemical species, a reactant A and an auto-catalyst B and C an inert chemical species.We use numerical computation to give more accurate estimates on minimum speed of traveling waves for autocatalytic reaction without decay, providing useful insight in the study of stability of traveling waves. For autocatalytic reaction of order $m = 2$ with linear decay $l = 1$, which hasa particular important role in biological pattern formation, it is shown numerically that there exist multiple traveling waves with 1, 2 and 3 peaks with certain choices of parameters.The second part of this thesis is on the global stability of diffusive predator-prey system of Leslie Type and Holling-Tanner Type in a bounded domain $\Omega\subset R^N$ with no-flux boundary condition. By using a new approach, we establish much improved global asymptotic stability of a unique positiveequilibrium solution. We also show the result can be extended to more general type of systems with heterogeneous environment and/or other kind of kinetic terms.
Show less - Date Issued
- 2016
- Identifier
- CFE0006519, ucf:51359
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006519
- Title
- The mauC gene encodes a versatile signal sequence and redox protein that can be utilized in native and non-native protein expression and electron trnasfer systems.
- Creator
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Dow, Brian, Davidson, Victor, Self, William, Rohde, Kyle, Tatulian, Suren, University of Central Florida
- Abstract / Description
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The redox-active type 1 copper site of amicyanin is composed of a single copper ion that is coordinated by two histidines, a methionine, and a cysteine residue. This redox site has a potential of +265 mV at pH7.5. Over ten angstroms away from the copper site resides a tryptophan residue whose fluorescence is quenched by the copper. The effects of the tryptophan on the electron transfer (ET) properties were investigated by site-directed mutagenesis. Lessons learned about the hydrogen bonding...
Show moreThe redox-active type 1 copper site of amicyanin is composed of a single copper ion that is coordinated by two histidines, a methionine, and a cysteine residue. This redox site has a potential of +265 mV at pH7.5. Over ten angstroms away from the copper site resides a tryptophan residue whose fluorescence is quenched by the copper. The effects of the tryptophan on the electron transfer (ET) properties were investigated by site-directed mutagenesis. Lessons learned about the hydrogen bonding network of amicyanin from the aforementioned study were attempted to be used as a model to increase the stability of another beta barrel protein, the immunoglobulin light chain variable domain (VL). In addition, amicyanin was used as an alternative redox partner with MauG. MauG is a diheme protein from the mau gene cluster that catalyzes the biogenesis of the tryptophan tryptophylquinone cofactor of methylamine dehydrogenase (MADH). The amicyanin-MauG complex was used to study the free energy dependence and impact of reorganization energy in biological electron transfer reactions.The sole tryptophan of amicyanin was converted to a tyrosine via site-directed mutagenesis. This mutation had no effect on the electron transfer parameters with its redox partners, methylamine dehydrogenase and cytochrome c-551i. However, the pKa of the pH-dependence of the redox potential of the copper site was shifted +0.5 pH units. This was a result of an additional hydrogen bond between Met51 and the copper coordinating residue His95 in the reduced form of amicyanin. This additional hydrogen bond stabilizes the reduced form. Also, the stability of the copper site and the protein overall was significantly decreased, as seen by the temperature dependence of the visible spectrum of the copper site and the circular dichroism spectrum of the protein. This destabilization is attributed to the loss of an interior, cross-barrel hydrogen bond.The VL is structurally similar to amicyanin, but it does not contain any cross-barrel hydrogen bonds. The importance of the cross-barrel hydrogen bond in stabilizing amicyanin is evident. A homologous bond in VL was attempted to be engineered by using site-directed mutagenesis to insert neutral residues with protonatable groups into the core of the protein. Wild-type (WT) VL was purified from the periplasm and found to be properly folded as determined by circular dichroism and size exclusion chromatography. Mutants were expressed in E. coli using the amicyanin signal sequence for periplasmic expression. Folded mutant protein could not be purified from the periplasm.When amicyanin is used in complex with MauG, it retains the pH-dependence of the redox potential of its copper site due to the looseness of the interprotein interface. The free energy of the reaction was manipulated by variation in pH from pH 5.8 to 8.0. The ET parameters are reorganization energy of 2.34 eV and an electronic coupling constant of 0.6 cm-1. P94A amicyanin has a potential that is 120 mV higher than WT amicyanin and was used to extend the range of the free energy dependence studied. The ET parameters of the reaction of WT and P94A amicyanin with MauG were within error of each other. This is significant because the ET reaction of P94A amicyanin with its natural electron acceptor was not able to be studied due to a kinetic coupling of the ET step with a non-ET step. This kinetic coupling obscured the parameters of the ET step because it is not kinetically distinguishable from the ET step.A Y294H MauG mutant was also studied. This mutation replaced the axial tyrosine ligand of the six-coordinate heme of MauG with a histidine. No reaction is observed with Y294H MauG in its native reaction. However, the high valent oxidation state of the five-coordinate heme of Y294H MauG reacts with reduced amicyanin. The ET rate was analyzed by ET theory to study the high valent heme in Y294H MauG. The reorganization energy of Y294H MauG was calculated to be nearly 20% lower as compared to the same reaction with WT MauG. These results provide insight into the obscured nature of reorganization energy of large redox cofactors in proteins, particularly heme cofactors, as well as to how the active sites of enzymes are optimized to perform long range ET vs catalysis with regard to balancing redox potential and reorganization energy.
Show less - Date Issued
- 2016
- Identifier
- CFE0006100, ucf:51192
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006100
- Title
- Catalytically Enhanced Heterogeneous Combustion of methane.
- Creator
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Terracciano, Anthony, Orlovskaya, Nina, Vasu Sumathi, Subith, Chow, Louis, Kassab, Alain, University of Central Florida
- Abstract / Description
-
Heterogeneous combustion is an advanced internal combustion technique, which enables heat recuperation within the flame by utilizing a highly porous ceramic media as a regenerator. Heat released within the gas phase convectively transfers to the solid media. This heat within the solid media then travels towards the inlet, enabling reactant preheating. Such heat redistribution enables stable burning of both ultra-lean fuel/air mixtures, forming a more diffuse flame through the combustion...
Show moreHeterogeneous combustion is an advanced internal combustion technique, which enables heat recuperation within the flame by utilizing a highly porous ceramic media as a regenerator. Heat released within the gas phase convectively transfers to the solid media. This heat within the solid media then travels towards the inlet, enabling reactant preheating. Such heat redistribution enables stable burning of both ultra-lean fuel/air mixtures, forming a more diffuse flame through the combustion chamber, and results in reduced pollutant formation. To further enhance heterogeneous combustion, the ceramic media can be coated with catalytically active materials, which facilitates surface based chemical reactions that could occur in parallel with gas phase reactions.Within this work, a flow stabilized heterogeneous combustor was designed and developed consisting of a reactant delivery nozzle, combustion chamber, and external instrumentation. The reactant delivery nozzle enables the combustor to operate on mixtures of air, liquid fuel, and gaseous fuel. Although this combustor has high fuel flexibility, only gaseous methane was used within the presented experiments. Within the reactant delivery nozzle, reactants flow through a tube mixer, and a homogeneous gaseous mixture is delivered to the combustion chamber. ?-alumina (?-Al2O3), magnesia stabilized zirconia (MgO-ZrO2), or silicon carbide (SiC) was used as the material for the porous media. Measurement techniques which were incorporated in the combustor include an array of axially mounted thermocouples, an external microphone, an external CCD camera, and a gas chromatograph with thermal conductivity detector which enable temperature measurements, acoustic spectroscopy, characterization of thermal radiative emissions, and composition analysis of exhaust gasses, respectively. Before evaluation of the various solid media in the combustion chamber the substrates and catalysts were characterized using X-ray diffraction, X-ray fluorescence, scanning electron microscopy and energy dispersive spectroscopy. MgO-ZrO2 porous media was found to outperform both ?-Al2O3 and SiC matrices, as it was established that higher temperatures for a given equivalence ratio were achieved when the flame was contained within a MgO-ZrO2 matrix. This was explained by the presence of oxygen vacancies within the MgO doped ZrO2 fluorite lattice which facilitated catalytic reactions. Several catalyst compositions were evaluated to promote combustion within a MgO-ZrO2 matrix even further.Catalysts such as: Pd enhanced WC, ZrB2, Ce0.80Gd0.20O1.90, LaCoO3, La0.80Ca0.20CoO3, La0.75Sr0.25Fe0.95Ru0.05O3, and La0.75Sr0.25Cr0.95Ru0.05O3; were evaluated under lean fuel/air mixtures. LaCoO3 outperformed all other catalysts, by enabling the highest temperatures within the combustion chamber, followed by Ce0.80Gd0.20O1.90. Both LaCoO3 and Ce0.80Gd0.20O1.90 enabled a flame to exist at ?=0.45(&)#177;0.02, however LaCoO3 caused the flame to be much more stable. Furthermore, it was discovered that the coating of MgO-ZrO2 with LaCoO3 significantly enhanced the total emissive power of the combustion chamber. In this work as acoustic spectroscopy was used to characterize heterogeneous combustion for the first time. It was found that there is a dependence of acoustic emission n the equivalence ratio and flame position regardless of media and catalyst combination. It was also found that when different catalysts were used, the acoustic tones produced during combustion at fixed reactant flow rates were distinct
Show less - Date Issued
- 2016
- Identifier
- CFE0006508, ucf:51364
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0006508
- Title
- DESIGN AND DEVELOPMENT OF HETEROGENOUS COMBUSTION SYSTEMS FOR LEAN BURN APPLICATIONS.
- Creator
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Terracciano, Anthony, Orlovskaya, Nina, Vasu Sumathi, Subith, Chow, Louis, Kassab, Alain, University of Central Florida
- Abstract / Description
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Combustion with a high surface area continuous solid immersed within the flame, referred to as combustion in porous media, is an innovative approach to combustion as the solid within the flame acts as an internal regenerator distributing heat from the combustion byproducts to the upstream reactants. By including the solid structure, radiative energy extraction becomes viable, while the solid enables a vast extension of flammability limits compared to conventional flames, while offering...
Show moreCombustion with a high surface area continuous solid immersed within the flame, referred to as combustion in porous media, is an innovative approach to combustion as the solid within the flame acts as an internal regenerator distributing heat from the combustion byproducts to the upstream reactants. By including the solid structure, radiative energy extraction becomes viable, while the solid enables a vast extension of flammability limits compared to conventional flames, while offering dramatically reduced emissions of NOx and CO, and dramatically increased burning velocities. Efforts documented within are used for the development of a streamlined set of design principles, and characterization of the flame's behavior when operating under such conditions, to aid in the development of future combustors for lean burn applications in open flow systems. Principles described herein were developed from a combination of experimental work and reactor network modeling using CHEMKIN-PRO. Experimental work consisted of a parametric analysis of operating conditions pertaining to reactant flow, combustion chamber geometric considerations and the viability of liquid fuel applications. Experimental behavior observed, when utilizing gaseous fuels, was then used to validate model outputs through comparing thermal outputs of both systems. Specific details pertaining to a streamlined chemical mechanism to be used in simulations, included within the appendix, and characterization of surface area of the porous solid are also discussed. Beyond modeling the experimental system, considerations are also undertaken to examine the applicability of exhaust gas recirculation and staged combustion as a means of controlling the thermal and environmental output of porous combustion systems. This work was supported by ACS PRF #51768-ND10 and NSF IIP 1343454.
Show less - Date Issued
- 2014
- Identifier
- CFE0005269, ucf:50549
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005269
