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Genome-Wide Survey And Expression Profiling Of Ccch-Zinc Finger Family Reveals A Functional Module In Macrophage Activation, Jian Liang, Wenjun Song, Gail Tromp, Pappachan E. Kolattukudy, Mingui Fu Jan 2008

Genome-Wide Survey And Expression Profiling Of Ccch-Zinc Finger Family Reveals A Functional Module In Macrophage Activation, Jian Liang, Wenjun Song, Gail Tromp, Pappachan E. Kolattukudy, Mingui Fu

Faculty Bibliography 2000s

Previously, we have identified a novel CCCH zinc finger protein family as negative regulators of macrophage activation. To gain an overall insight into the entire CCCH zinc finger gene family and to evaluate their potential role in macrophage activation, here we performed a genome-wide survey of CCCH zinc finger genes in mouse and human. Totally 58 CCCH zinc finger genes in mouse and 55 in human were identified and most of them have not been reported previously. Phylogenetic analysis revealed that the mouse CCCH family was divided into 6 groups. Meanwhile, we employed quantitative real-time PCR to profile their tissue …

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A Novel Ccch-Zinc Finger Protein Family Regulates Proinflammatory Activation Of Macrophages, Jian Liang, Jing Wang, Asim Azfer, Wenjun Song, Gail Tromp, Pappachan E. Kolattukudy, Mingui Fu Jan 2008

A Novel Ccch-Zinc Finger Protein Family Regulates Proinflammatory Activation Of Macrophages, Jian Liang, Jing Wang, Asim Azfer, Wenjun Song, Gail Tromp, Pappachan E. Kolattukudy, Mingui Fu

Faculty Bibliography 2000s

Activated macrophages play an important role in many inflammatory diseases. However, the molecular mechanisms controlling macrophage activation are not completely understood. Here we report that a novel CCCH-zinc finger protein family, MCPIP1, 2, 3, and 4, encoded by four genes, Zc3h12a, Zc3h12b, Zc3h12c, and Zc3h12d, respectively, regulates macrophage activation. Northern blot analysis revealed that the expression of MCPIP1 and MCPIP3 was highly induced in macrophages in response to treatment with lipopolysaccharide (LPS). Although not affecting cell surface marker expression and phagocytotic function, overexpression of MCPIP1 significantly blunted LPS-induced inflammatory cytokine and NO(2)radical anion. production as well as their gene expression. …

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Migration And Luminescence Enhancement Effects Of Deuterium In Zno/Zncdo Quantum Wells, W. Lim, D. P. Norton, S. J. Pearton, X. J. Wang, W. M. Chen, I. A. Buyanova, A. Osinsky, J. W. Dong, B. Hertog, A. V. Thompson, W. V. Schoenfeld, Y. L. Wang, F. Ren Jan 2008

Migration And Luminescence Enhancement Effects Of Deuterium In Zno/Zncdo Quantum Wells, W. Lim, D. P. Norton, S. J. Pearton, X. J. Wang, W. M. Chen, I. A. Buyanova, A. Osinsky, J. W. Dong, B. Hertog, A. V. Thompson, W. V. Schoenfeld, Y. L. Wang, F. Ren

Faculty Bibliography 2000s

ZnO/ZnCdO/ZnO multiple quantum well samples grown on sapphire substrates by molecular beam epitaxy and annealed in situ were exposed to D(2) plasmas at 150 degrees C. The deuterium showed migration depths of similar to 0.8 mu m for 30 min plasma exposures, with accumulation of (2)H in the ZnCdO wells. The photoluminescence (PL) intensity from the samples was increased by factors of 5 at 5 K and similar to 20 at 300 K as a result of the deuteration, most likely due to passivation of competing nonradiative centers. Annealing up to 300 degrees C led to increased migration of (2)H …

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Dynamics Of Dna Translocation Through An Attractive Nanopore, Kaifu Luo, Tapio Ala-Nissila, See-Chan Ying, Aniket Bhattacharya Jan 2008

Dynamics Of Dna Translocation Through An Attractive Nanopore, Kaifu Luo, Tapio Ala-Nissila, See-Chan Ying, Aniket Bhattacharya

Faculty Bibliography 2000s

We investigate the dynamics of single-stranded DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases A and C, having different base-pore interactions, e.g., a strong (weak) attractive force between the pore and the base A (C) inside the pore. From a series of studies on hetero-DNAs with repeat units A(m)C(n), we find that the translocation time decreases exponentially as a function of the volume fraction f(C) of …

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Translocation Dynamics With Attractive Nanopore-Polymer Interactions, Kaifu Luo, Tapio Ala-Nissila, See-Chen Ying, Aniket Bhattacharya Jan 2008

Translocation Dynamics With Attractive Nanopore-Polymer Interactions, Kaifu Luo, Tapio Ala-Nissila, See-Chen Ying, Aniket Bhattacharya

Faculty Bibliography 2000s

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time tau approximate to tau(1)+tau(2)+tau(3) corresponding to the initial filling of the pore, transfer of polymer from the cis side to the trans side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from nonactivated to activated in nature as the strength of the …

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Dynamical Scaling Exponents For Polymer Translocation Through A Nanopore, Kaifu Luo, Santtu T. T. Ollila, Ilkka Huopaniemi, Tapio Ala-Nissila, Pawel Pomorski, Mikko Karttunen, See-Chen Ying, Aniket Bhattacharya Jan 2008

Dynamical Scaling Exponents For Polymer Translocation Through A Nanopore, Kaifu Luo, Santtu T. T. Ollila, Ilkka Huopaniemi, Tapio Ala-Nissila, Pawel Pomorski, Mikko Karttunen, See-Chen Ying, Aniket Bhattacharya

Faculty Bibliography 2000s

We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time tau similar to N-alpha and the mean-square change of the PT coordinate, < s(2)(t) > similar to t(beta). We find alpha=1+2 nu and beta=2/alpha for unbiased PT in two dimensions (2D) and three dimensions (3D). The relation alpha beta=2 holds for driven PT in 2D, with a crossover from alpha approximate to 2 nu for short chains to alpha approximate to 1+nu for …

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Androgen Regulates Cdc6 Transcription Through Interactions Between Androgen Receptor And E2f Transcription Factor In Prostate Cancer Cells, Ipsita Mallik, Monica Davila, Tenekua Tapia, Brian Schanen, Ratna Chakrabarti Jan 2008

Androgen Regulates Cdc6 Transcription Through Interactions Between Androgen Receptor And E2f Transcription Factor In Prostate Cancer Cells, Ipsita Mallik, Monica Davila, Tenekua Tapia, Brian Schanen, Ratna Chakrabarti

Faculty Bibliography 2000s

Androgen receptor plays a critical role in the development and maintenance of cancers in the prostate. Earlier, we have shown that Cdc6, a regulatory protein for initiation of DNA replication, is down regulated in androgen-insensitive prostate cancer cells. In this report, we studied the involvement of androgen, mediated through androgen receptor (AR) in regulation of Cdc6 expression. Our results demonstrated that androgen treatment stimulated Cdc6 expression in xenograft tumors and androgen-sensitive prostate cancer cells. We also showed that androgen treatment stimulated Cdc6 transcription through possible interaction of AR with the ARE sequence in the Cdc6 promoter and that the stimulatory …

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Sequence Specificity Of Bal 31 Nuclease For Ssdna Revealed By Synthetic Oligomer Substrates Containing Homopolymeric Guanine Tracts, April Marrone, Jack Ballantyne Jan 2008

Sequence Specificity Of Bal 31 Nuclease For Ssdna Revealed By Synthetic Oligomer Substrates Containing Homopolymeric Guanine Tracts, April Marrone, Jack Ballantyne

Faculty Bibliography 2000s

Background: The extracellular nuclease from Alteromonas espejiana, BAL 31 catalyzes the degradation of single-stranded and linear duplex DNA to 5'-mononucleotides, cleaves negatively supercoiled DNA to the linear duplex form, and cleaves duplex DNA in response to the presence of apurinic sites. Principal Findings: In this work we demonstrate that BAL 31 activity is affected by the presence of guanine in singlestranded DNA oligomers. Specifically, nuclease activity is shown to be affected by guanine's presence in minimal homopolymeric tracts in the middle of short oligomer substrates and also by its presence at the 39 end of ten and twenty base oligomers. …

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Double Excitations And State-To-State Transition Dipoles In Pi-Pi* Excited Singlet States Of Linear Polyenes: Time-Dependent Density-Functional Theory Versus Multiconfigurational Methods, Ivan A. Mikhailov, Sergio Tafur, Artëm E. Masunov Jan 2008

Double Excitations And State-To-State Transition Dipoles In Pi-Pi* Excited Singlet States Of Linear Polyenes: Time-Dependent Density-Functional Theory Versus Multiconfigurational Methods, Ivan A. Mikhailov, Sergio Tafur, Artëm E. Masunov

Faculty Bibliography 2000s

The effect of static and dynamic electron correlation on the nature of excited states and state-to-state transition dipole moments is studied with a multideterminant wave function approach on the example of all-trans linear polyenes (C4H6, C6H8, and C8H10). Symmetry-forbidden singlet nA(g) states were found to separate into three groups: purely single, mostly single, and mostly double excitations. The excited-state absorption spectrum is dominated by two bright transitions: 1B(u)-2A(g) and 1B(u)-mA(g), where mA(g) is the state, corresponding to two-electron excitation from the highest occupied to lowest unoccupied molecular orbital. The richness of the excited-state absorption spectra and strong mixing of the …

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Chromosomal Evidence For A Putative Cryptic Species In The Gymnotus Carapo Species-Complex (Gymnotiformes, Gymnotidae), Susana Sr Milhomem, Julio C. Pieczarka, William Gr Crampton, Danillo S. Silva, Augusto Cp De Souza, Jaime R. Carvalho Jr., Cleusa Y. Nagamachi Jan 2008

Chromosomal Evidence For A Putative Cryptic Species In The Gymnotus Carapo Species-Complex (Gymnotiformes, Gymnotidae), Susana Sr Milhomem, Julio C. Pieczarka, William Gr Crampton, Danillo S. Silva, Augusto Cp De Souza, Jaime R. Carvalho Jr., Cleusa Y. Nagamachi

Faculty Bibliography 2000s

Background: In this study we examined the karyotypes of morphologically indistinguishable populations of the electric knifefish Gymnotus carapo sensu stricto from the Eastern Amazon of Brazil. These were identified unambiguously on the basis of external morphology, meristics, and pigmentation. Results: Specimens from one of five localities exhibited a karyotype previously not documented for Gymnotus species in the Amazon basin: 2n = 40 (34M/SM+6ST/A). Samples from the other four localities exhibited a different karyotype: 2n = 42 (30M/SM+12ST/A), which we had previously described. Specimens from all five localities presented constitutive heterochromatin in the centromeric region of almost all chromosomes, including in …

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Revisiting The Mechanism Of Macrolide-Antibiotic Resistance Mediated By Ribosomal Protein L22, Sean D. Moore, Robert T. Sauer Jan 2008

Revisiting The Mechanism Of Macrolide-Antibiotic Resistance Mediated By Ribosomal Protein L22, Sean D. Moore, Robert T. Sauer

Faculty Bibliography 2000s

Bacterial antibiotic resistance can occur by many mechanisms. An intriguing class of mutants is resistant to macrolide antibiotics even though these drugs still bind to their targets. For example, a 3-residue deletion (Delta MKR) in ribosomal protein L22 distorts a loop that forms a constriction in the ribosome exit tunnel, apparently allowing nascent-chain egress and translation in the presence of bound macrolides. Here, however, we demonstrate that Delta MKR and wild-type ribosomes show comparable macrolide sensitivity in vitro. In Escherichia coli, we find that this mutation reduces antibiotic occupancy of the target site on ribosomes in a manner largely dependent …

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Methyl Farnesoate Couples Environmental Changes To Testicular Development In The Crab Carcinus Maenas, G. P. C. Nagaraju, D. W. Borst Jan 2008

Methyl Farnesoate Couples Environmental Changes To Testicular Development In The Crab Carcinus Maenas, G. P. C. Nagaraju, D. W. Borst

Faculty Bibliography 2000s

Carcinus maenas males have two major color phases. Green-phase males molt frequently and tend to live in brackish estuaries during the summer. After becoming red-phase males, they molt infrequently, have higher mating success, and live in cooler, deeper water. We found profound differences between these two phases in the way salinity and temperature affect hemolymph levels of methyl farnesoate (MF), a hormone that affects crustacean reproduction. Few green-phase males ( < 10%) had detectable MF in 33 ppt seawater (SW) at 11 or 18 degrees C. By contrast, about 30% of the red-phase males had detectable MF at either temperature. After transfer to 5 ppt SW, none of the green-phase males had detectable MF at 11 degrees C whereas 100% of green-phase males did at 18 degrees C. By contrast, 100% of the red-phase males had detectable MF in 5 ppt SW at either temperature. At 11 degrees C, green-phase males had detectable MF after eyestalk ablation (ESA), showing that they can produce MF. There was no additional increase in MF levels when ESA animals of either color phase were transferred to 5 ppt SW, suggesting that the eyestalk is the primary regulator of the MF response to low salinity. MF levels of green-phase males were increased by injecting MF, by ESA, or by exposure to 5 ppt SW at 18 degrees C. The testicular index of these treated animals nearly doubled after two weeks. Our results strongly suggest that environmental conditions such as temperature and salinity, affect testicular development in this crab by changing its MF levels.

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Therapeutic Modulation Of Apoptosis: Targeting The Bcl-2 Family At The Interface Of The Mitochondrial Membrane, Kathleen N. Nemee, Annette R. Khaled Jan 2008

Therapeutic Modulation Of Apoptosis: Targeting The Bcl-2 Family At The Interface Of The Mitochondrial Membrane, Kathleen N. Nemee, Annette R. Khaled

Faculty Bibliography 2000s

A vast portion of human disease results when the process of apoptosis is defective. Disorders resulting from inappropriate cell death range from autoimmune and neurodegenerative conditions to heart disease. Conversely, prevention of apoptosis is the hallmark of cancer and confounds the efficacy of cancer therapeutics. In the search for optimal targets that would enable the control of apoptosis, members of the BCL-2 family of anti- and pro-apoptotic factors have figured prominently. Development of BCL-2 antisense approaches, small molecules, and BH3 peptidomimetics has met with both success and failure. Success-because BCL-2 proteins play essential roles in apoptosis. Failure-because single targets for …

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Monocyte Chemotactic Protein (Mcp)-1 Promotes Angiogenesis Via A Novel Transcription Factor, Mcp-1-Induced Protein (Mcpip), Jianli Niu, Asim Azfer, Olga Zhelyabovska, Sumbul Fatma, Pappachan E. Kolattukudy Jan 2008

Monocyte Chemotactic Protein (Mcp)-1 Promotes Angiogenesis Via A Novel Transcription Factor, Mcp-1-Induced Protein (Mcpip), Jianli Niu, Asim Azfer, Olga Zhelyabovska, Sumbul Fatma, Pappachan E. Kolattukudy

Faculty Bibliography 2000s

Monocyte chemotactic protein-1 (MCP-1) has been recognized as an angiogenic chemokine. The molecular mechanism of MCP-1-mediated angiogenesis remains unknown. We recently identified a novel transcription factor, designated MCP-1-induced protein (MCPIP), in human monocytes after treatment with MCP-1. We investigated whether MCP-1-induced angiogenesis is mediated via MCPIP. Treatment of human umbilical vein endothelial cells (HUVECs) with MCP-1 induced expression of MCPIP and capillary-like tube formation. Knockdown of MCPIP by small interfering RNA (siRNA) suppressed MCP-1-induced angiogenesis-related gene VEGF and HIF-1 alpha expression as well as tube formation. Transfection of HUVECs with an MCPIP expression vector induced angiogenesis-related genes and tube formation. …

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Demonstration Of Three-Dimensional Optical Imaging Using A Confocal Microscope Based On A Liquid-Crystal Electronic Lens, Nabeel A. Riza, Mumtaz Sheikh, Grady Webb-Wood, Pieter G. Kik Jan 2008

Demonstration Of Three-Dimensional Optical Imaging Using A Confocal Microscope Based On A Liquid-Crystal Electronic Lens, Nabeel A. Riza, Mumtaz Sheikh, Grady Webb-Wood, Pieter G. Kik

Faculty Bibliography 2000s

Three-dimensional (3-D) imaging is demonstrated using an electronically controlled liquid crystal (LC) optical lens to accomplish a no-moving-parts depth-section scanning in a modified commercial 3-D confocal microscope. Specifically, 3-D views of a standard CDC blood vessel (enclosed in a glass slide) have been obtained using the modified confocal microscope operating at the red 633-nm laser wavelength. The image sizes over a 25-mu m axial scan depth were 50 x 50 mu m and 80 x 80 mu m, using 60x and 20x micro-objectives, respectively. The transverse motion step was 0.1 mu m for the 60x data and 0.2 mu m …

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Species-Specific Diversity Of A Fixed Motor Pattern: The Electric Organ Discharge Of Gymnotus, Alejo Rodrìguez-Cattaneo, Ana Carolina Pereira, Pedro A. Aguilera, William G. R. Crampton, Angel A. Caputi Jan 2008

Species-Specific Diversity Of A Fixed Motor Pattern: The Electric Organ Discharge Of Gymnotus, Alejo Rodrìguez-Cattaneo, Ana Carolina Pereira, Pedro A. Aguilera, William G. R. Crampton, Angel A. Caputi

Faculty Bibliography 2000s

Understanding fixed motor pattern diversity across related species provides a window for exploring the evolution of their underlying neural mechanisms. The electric organ discharges of weakly electric fishes offer several advantages as paradigmatic models for investigating how a neural decision is transformed into a spatiotemporal pattern of action. Here, we compared the far fields, the near fields and the electromotive force patterns generated by three species of the pulse generating New World gymnotiform genus Gymnotus. We found a common pattern in electromotive force, with the far field and near field diversity determined by variations in amplitude, duration, and the degree …

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Heat Stress In The Intertidal: Comparing Survival And Growth Of An Invasive And Native Mussel Under A Variety Of Thermal Conditions, Kimberly R. Schneider Jan 2008

Heat Stress In The Intertidal: Comparing Survival And Growth Of An Invasive And Native Mussel Under A Variety Of Thermal Conditions, Kimberly R. Schneider

Faculty Bibliography 2000s

In the rocky intertidal, organisms frequently experience a wide range of daily body temperatures depending on the stage of the tide and the time of day. In the intertidal, the thermal adaption of a species and its ability to invade a new region may be closely linked. In this research, the physiological effects of thermal stress in both low tide and high tide conditions are compared between Mytilus galloprovincialis, a worldwide mussel invader, and M. trossulus, a sibling species. In a seawater tank, mussels were exposed to one of three aerial temperature treatments (20, 25, 30 degrees C) in a …

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Codon Choice In Genes Depends On Flanking Sequence Information - Implications For Theoretical Reverse Translation, Karthikeyan Sivaraman, Aswinsainarain Seshasayee, Patrick M. Tarwater, Alexander M. Cole Jan 2008

Codon Choice In Genes Depends On Flanking Sequence Information - Implications For Theoretical Reverse Translation, Karthikeyan Sivaraman, Aswinsainarain Seshasayee, Patrick M. Tarwater, Alexander M. Cole

Faculty Bibliography 2000s

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods …

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Genome Sequencing And Analysis Reveals Possible Determinants Of Staphylococcus Aureus Nasal Carriage, Karthikeyan Sivaraman, Nitya Venkataraman, Jennifer Tsai, Scott Dewell, Alexander M. Cole Jan 2008

Genome Sequencing And Analysis Reveals Possible Determinants Of Staphylococcus Aureus Nasal Carriage, Karthikeyan Sivaraman, Nitya Venkataraman, Jennifer Tsai, Scott Dewell, Alexander M. Cole

Faculty Bibliography 2000s

Background: Nasal carriage of Staphylococcus aureus is a major risk factor in clinical and community settings due to the range of etiologies caused by the organism. We have identified unique immunological and ultrastructural properties associated with nasal carriage isolates denoting a role for bacterial factors in nasal carriage. However, despite extensive molecular level characterizations by several groups suggesting factors necessary for colonization on nasal epithelium, genetic determinants of nasal carriage are unknown. Herein, we have set a genomic foundation for unraveling the bacterial determinants of nasal carriage in S. aureus. Results: MLST analysis revealed no lineage specific differences between carrier …

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Stochastic Sensing Of Relative Anisotropic Polarizabilities, S. Sukhov, D. Haefner, A. Dogariu Jan 2008

Stochastic Sensing Of Relative Anisotropic Polarizabilities, S. Sukhov, D. Haefner, A. Dogariu

Faculty Bibliography 2000s

We describe the concept of stochastic scattering polarimetry. This method allows determination of the anisotropic polarizability of a scattering object using a statistical analysis of the polarimetrically measured intensity distributions in the wave zone (far field). We show that this anisotropic polarizability may be determined even in situations where the state of polarization of the incident field is not known. The efficiency of the recovering procedure is demonstrated by several examples of light scattering in both far- and near-field geometries.

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Coupled Dipole Method For Modeling Optical Properties Of Large-Scale Random Media, S. Sukhov, D. Haefner, A. Dogariu Jan 2008

Coupled Dipole Method For Modeling Optical Properties Of Large-Scale Random Media, S. Sukhov, D. Haefner, A. Dogariu

Faculty Bibliography 2000s

We present an extension of the coupled dipole approximation technique to model optical properties of large-scale slabs of homogeneous and inhomogeneous materials. This method is based on a modification of the Green's function to take into account the interaction between dipoles located at arbitrary distances within the slab. This method allows modeling of various aspects of the structural morphology of composite materials, including component size and spatial distribution as well as surface roughness effects. Our procedure provides an adequate description of far-field optical properties such as the specular and diffuse reflection of light.

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Elastic Modulus Of Viral Nanotubes, Yue Zhao, Zhibin Ge, Jiyu Fang Jan 2008

Elastic Modulus Of Viral Nanotubes, Yue Zhao, Zhibin Ge, Jiyu Fang

Faculty Bibliography 2000s

We report an experimental and theoretical study of the radial elasticity of tobacco mosaic virus (TMV) nanotubes. An atomic force microscope tip is used to apply small radial indentations to deform TMV nanotubes. The initial elastic response of TMV nanotubes can be described by finite-element analysis in 5 nm indentation depths and Hertz theory in 1.5 nm indentation depths. The derived radial Young's modulus of TMV nanotubes is 0.92 +/- 0.15 GPa from finite-element analysis and 1.0 +/- 0.2 GPa from the Hertz model, which are comparable with the reported axial Young's modulus of 1.1 GPa [Falvo et al., Biophys. …

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Femtosecond Laser Photo-Response Of Ge23sb7s70 Films, Troy Anderson, Laeticia Petit, Nathan Calie, Jiyeon Choi, Juejun Hu, Anu Agarwal, Lionel Kimberling, Kathleen Richardson, Martin Richardson Jan 2008

Femtosecond Laser Photo-Response Of Ge23sb7s70 Films, Troy Anderson, Laeticia Petit, Nathan Calie, Jiyeon Choi, Juejun Hu, Anu Agarwal, Lionel Kimberling, Kathleen Richardson, Martin Richardson

Faculty Bibliography 2000s

Ternary chalcogenide glass films from identical parent bulk glasses were prepared by thermal evaporation (TE) and pulsed laser deposition (PLD) and subjected to 810-nm femtosecond laser exposure at both kHz and MHz repetition rates. The exposure-induced modification on the glass film's surface profile, refractive index, and structural properties were shown to be a function of laser irradiance, the number of laser pulses per focal spot, and repetition rate. Film response was shown to be related to deposition technique-related density and the number of glass bonds within the irradiated focal volume. The induced changes resulted from a reduction in glass network …

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Bats: A Bayesian User-Friendly Software For Analyzing Time Series Microarray Experiments, Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky Jan 2008

Bats: A Bayesian User-Friendly Software For Analyzing Time Series Microarray Experiments, Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky

Faculty Bibliography 2000s

Background: Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may depend on time. One of the goals of modern molecular biology is the high-throughput identification of genes associated with a particular treatment or a biological process of interest. From methodological and computational point of view, analyzing high-dimensional time course microarray data requires very specific set of tools which are usually not included in standard software packages. Recently, the authors of this paper developed a fully Bayesian approach …

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Effective Plague Vaccination Via Oral Delivery Of Plant Cells Expressing F1-V Antigens In Chloroplasts, Philip A. Arlen, Michael Singleton, Jeffrey J. Adamovicz, Yi Ding, Abdolreza Davoodi-Semiromi, Henry Daniell Jan 2008

Effective Plague Vaccination Via Oral Delivery Of Plant Cells Expressing F1-V Antigens In Chloroplasts, Philip A. Arlen, Michael Singleton, Jeffrey J. Adamovicz, Yi Ding, Abdolreza Davoodi-Semiromi, Henry Daniell

Faculty Bibliography 2000s

The chloroplast bioreactor is an alternative to fermentation-based systems for production of vaccine antigens and biopharmaceuticals. We report here expression of the plague FIN fusion antigen in chloroplasts. Site-specific transgene integration and homoplasmy were confirmed by PCR and Southern blotting. Mature leaves showed the highest level of transgene expression on the third day of continuous illumination, with a maximum level of 14.8% of the total soluble protein. Swiss Webster mice were primed with adjuvant-containing subcutaneous (s.c.) doses of F1-V and then boosted with either adjuvanted s.c. doses (s.c. FIN mice) or unadjuvanted oral doses (oral F1-V mice). Oral FIN mice …

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Correlation Between Rpob Gene Mutation In Mycobacterium Avium Subspecies Paratuberculosis And Clinical Rifabutin And Rifampicin Resistance For Treatment Of Crohn's Disease, Daniel R. Beckler, Sammer Elwasila, George Ghobrial, John F. Valentine, Saleh A. Naser Jan 2008

Correlation Between Rpob Gene Mutation In Mycobacterium Avium Subspecies Paratuberculosis And Clinical Rifabutin And Rifampicin Resistance For Treatment Of Crohn's Disease, Daniel R. Beckler, Sammer Elwasila, George Ghobrial, John F. Valentine, Saleh A. Naser

Faculty Bibliography 2000s

AIM: To investigate overlapping regions of the rpoB gene previously involved with rifamycin resistance in M. tuberculosis and seek correlation between rpoB mutations in clinical MAP strains with susceptibility to RIF and RFB. METHODS: We designed a molecular-based PCR method for the evaluation of rifabutin (RFB) and rifampicin (RIF) resistance based on probable determinant regions within the rpoB gene of MAP, including the 81 bp variable site located between nucleotides 1363 and 1443. The minimum inhibitory concentration (MIC) for RIF was also determined against 11 MAP isolates in attempt to seek correlation with rpoB sequences. RESULTS: We determined that MAP …

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Environmental And Biological Controls On Water And Energy Exchange In Florida Scrub Oak And Pine Flatwoods Ecosystems, Rosvel Bracho, Thomas L. Powell, Sabina Dore, Jiahong Li, C. Ross Hinkle, Bert G. Drake Jan 2008

Environmental And Biological Controls On Water And Energy Exchange In Florida Scrub Oak And Pine Flatwoods Ecosystems, Rosvel Bracho, Thomas L. Powell, Sabina Dore, Jiahong Li, C. Ross Hinkle, Bert G. Drake

Faculty Bibliography 2000s

Scrub oak and pine flatwoods are two contrasting ecosystems common to the humid subtropical climate of Florida. Scrub oak forests are short in stature (<2 >m) and occur on well-drained sandy soils, and pine flatwoods are much taller and occur in areas with poorly drained soils. Eddy covariance measurements were made from January 2001 to February 2003 over a scrub oak forest and from January 2002 to February 2003 over an adjacent pine flatwoods located on in central Florida, USA, and exposed to similar atmospheric conditions to evaluate how the dynamics of latent heat (lambda E) and sensible heat (H) …

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Identifying Non-Stationarities In Random Em Fields: Are Speckles Really Disturbing?, John Broky, Jeremy Ellis, Aristide Dogariu Jan 2008

Identifying Non-Stationarities In Random Em Fields: Are Speckles Really Disturbing?, John Broky, Jeremy Ellis, Aristide Dogariu

Faculty Bibliography 2000s

In dealing with random EM fields, ensemble averaging is an ubiquitous procedure. However, we demonstrate that spatial non-stationarities such as enhanced backscattering can be identified even from one single realization (snapshot) of the wave interaction with a random medium. Fourth-order correlations between field components at two different spatial points are shown to provide the necessary information.

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Self-Healing Properties Of Optical Airy Beams, John Broky, Georgios A. Siviloglou, Aristide Dogariu, Demetrios N. Christodoulides Jan 2008

Self-Healing Properties Of Optical Airy Beams, John Broky, Georgios A. Siviloglou, Aristide Dogariu, Demetrios N. Christodoulides

Faculty Bibliography 2000s

We investigate both theoretically and experimentally the self-healing properties of accelerating Airy beams. We show that this class of waves tends to reform during propagation in spite of the severity of the imposed perturbations. In all occasions the reconstruction of these beams is interpreted through their internal transverse power flow. The robustness of these optical beams in scattering and turbulent environments is also studied experimentally. Our observations are in excellent agreement with numerical simulations.

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The Gendered Altar: Wiccan Concepts Of Gender And Ritual Objects, Jesse Sloan Jan 2008

The Gendered Altar: Wiccan Concepts Of Gender And Ritual Objects, Jesse Sloan

Electronic Theses and Dissertations

Many ethnographic accounts within the annals of anthropological literature describe the religious beliefs and magical rituals of peoples throughout the world. Fewer scholars have focused on the relatively young Neo-Pagan religious movement. "Neo-Pagan," explains Helen Berger in Voices from the Pagan Census (2003), "is an umbrella term covering sects of a new religious movement, the largest and most important form of which is…Wicca" (Berger et al. 2003: 1). This thesis examines the relationship between practice and ideology by analyzing the material culture of Wiccan altars as used by Wiccans in Central Florida, USA. Particular attention is paid to beliefs …

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