DNA-mediated oxidation of transcription factor p53

Transcription factor p53 is the most commonly altered gene in human cancer. As a redox-active protein in direct contact with DNA, p53 can directly sense oxidative stress through DNA-mediated charge transport. Electron hole transport occurs with a shallow distance dependence over long distances through the π-stacked DNA bases, leading to the oxidation and dissociation of DNA-bound p53. The extent of p53 dissociation depends upon the redox potential of the response element DNA in direct contact with each p53 monomer. The DNA sequence dependence of p53 oxidative dissociation was examined by electrophoretic mobility shift assays using radiolabeled oligonucleotides containing both synthetic and human p53 response elements with an appended anthraquinone photooxidant. Greater p53 dissociation is observed from DNA sequences containing low redox potential purine regions, particularly guanine triplets, within the p53 response element. Using denaturing polyacrylamide gel electrophoresis of irradiated anthraquinone-modified DNA, the DNA damage sites, which correspond to locations of preferred electron hole localization, were determined. The resulting DNA damage preferentially localizes to guanine doublets and triplets within the response element. Oxidative DNA damage is inhibited in the presence of p53, however, only at DNA sites within the response element, and therefore in direct contact with p53. From these data, predictions about the sensitivity of human p53-binding sites to oxidative stress, as well as possible biological implications, have been made. On the basis of our data, the guanine pattern within the purine region of each p53-binding site determines the response of p53 to DNA-mediated oxidation, yielding for some sequences the oxidative dissociation of p53 from a distance and thereby providing another potential role for DNA charge transport chemistry within the cell.

To determine whether the change in p53 response element occupancy observed in vitro also correlates in cellulo, chromatin immunoprecipition (ChIP) and quantitative PCR (qPCR) were used to directly quantify p53 binding to certain response elements in HCT116N cells. The HCT116N cells containing a wild type p53 were treated with the photooxidant [Rh(phi)2bpy]³⁺, Nutlin-3 to upregulate p53, and subsequently irradiated to induce oxidative genomic stress. To covalently tether p53 interacting with DNA, the cells were fixed with disuccinimidyl glutarate and formaldehyde. The nuclei of the harvested cells were isolated, sonicated, and immunoprecipitated using magnetic beads conjugated with a monoclonal p53 antibody. The purified immounoprecipiated DNA was then quantified via qPCR and genomic sequencing. Overall, the ChIP results were significantly varied over ten experimental trials, but one trend is observed overall: greater variation of p53 occupancy is observed in response elements from which oxidative dissociation would be expected, while significantly less change in p53 occupancy occurs for response elements from which oxidative dissociation would not be anticipated.

The chemical oxidation of transcription factor p53 via DNA CT was also investigated with respect to the protein at the amino acid level. Transcription factor p53 plays a critical role in the cellular response to stress stimuli, which may be modulated through the redox modulation of conserved cysteine residues within the DNA-binding domain. Residues within p53 that enable oxidative dissociation are herein investigated. Of the 8 mutants studied by electrophoretic mobility shift assay (EMSA), only the C275S mutation significantly decreased the protein affinity (KD) for the Gadd45 response element. EMSA assays of p53 oxidative dissociation promoted by photoexcitation of anthraquinone-tethered Gadd45 oligonucleotides were used to determine the influence of p53 mutations on oxidative dissociation; mutation to C275S severely attenuates oxidative dissociation while C277S substantially attenuates dissociation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide labeled, while oxidized cysteines participating in disulfide bonds were ¹³C₂D₂-iodoacetamide labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed using a QTRAP 6500 LC-MS/MS system, quantified with Skyline, and directly compared. A distinct shift in peptide labeling toward ¹³C₂D₂-iodoacetamide labeled cysteines is observed in oxidized samples as compared to the respective controls. All of the observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds potentially among the C124, C135, C141, C182, C275, and C277. Based on these data it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.

DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

Visual pattern recognition network: Its training algorithm and its optoelectronic architecture

A visual pattern recognition network and its training algorithm are proposed. The network constructed of a one-layer morphology network and a two-layer modified Hamming net. This visual network can implement invariant pattern recognition with respect to image translation and size projection. After supervised learning takes place, the visual network extracts image features and classifies patterns much the same as living beings do. Moreover we set up its optoelectronic architecture for real-time pattern recognition. (C) 1996 Optical Society of America

Hit-or-miss representation of a pattern spectrum and its optical implementation

We demonstrate that a pattern spectrum can be decomposed into the union of hit-or-miss transforms with respect to a series of structure-element pairs. Moreover we use a Boolean-logic function to express the pattern spectrum and show that the Boolean-logic representation of a pattern spectrum is composed of hit-or-miss min terms. The optical implementation of a pattern spectrum is based on an incoherent optical correlator with a feedback operation. (C) 1996 Optical Society of America

Ultrafast temporal pattern generation and recognition

Ultrafast temporal pattern generation and recognition with femtosecond laser technology is presented, analyzed, and experimentally implemented. Ultrafast temporal pattern generation and recognition are realized by taking advantage of two well-known techniques: the space-time conversion technique and the ultrafast pulse measurement technique. Here the temporal pattern for the designed multiple pulses, optimized with a preassumed Gaussian spectral distribution of an ultrashort pulse, is described. With the simulation of a Gaussian spectral distribution, we realize that the uniformity of the generated multiple ultrafast temporal pulses is relevant to the repeated number of modulation periods in the mask in the spectral plane. Moreover, the change of Gaussian spectral phases with the wavelengths in the modulated phase plate is considered. Experiments of ultrafast temporal pattern recognition by the frequency-resolved optical gating (FROG) characterization technique are also given. (C) 2004 Society of Photo-Optical Instrumentation Engineers.

Aspects of the washout of salmonid eggs. 1. Observations on the physical characteristics of real and artificial eggs, their rate of fall in a water column and their pattern of settlement in an experimental channel

When salmonid redds are disrupted by spates, the displaced eggs will drift downstream. The mean distance of travel, the types of locations in which the eggs resettle and the depth of reburial of displaced eggs are not known. Investigation of these topics under field conditions presents considerable practical problems, though the use of artificial eggs might help to overcome some of them. Attempts to assess the similarities and/or differences in performance between real and artificial eggs are essential before artificial eggs can validly be used to simulate real eggs. The present report first compares the two types of egg in terms of their measurable physical characteristics (e.g. dimensions and density). The rate at which eggs fall in still water will relate to the rate at which they are likely to resettle in flowing water in the field. As the rate of fall will be influenced by a number of additional factors (e.g. shape and surface texture) which are not easily measured directly, the rates of fall of the two types of egg have been compared directly under controlled conditions. Finally, comparisons of the pattern of settlement of the two types of egg in flowing water in an experimental channel have been made. Although the work was primarily aimed at testing the value of artificial eggs as a simulation of real eggs, several side issues more directly concerned with the properties of real eggs and the likely distance of drift in natural streams have also been explored. This is the first of three reports made on this topic by the author in 1984.

Steady surface wave pattern in a shear flow

The subject under investigation concerns the steady surface wave patterns created by small concentrated disturbances acting on a non-uniform flow of a heavy fluid. The initial value problem of a point disturbance in a primary flow having an arbitrary velocity distribution (U(y), 0, 0) in a direction parallel to the undisturbed free surface is formulated. A geometric optics method and the classical integral transformation method are employed as two different methods of solution for this problem. Whenever necessary, the special case of linear shear (i.e. U(y) = 1+ϵy)) is chosen for the purpose of facilitating the final integration of the solution.

The asymptotic form of the solution obtained by the method of integral transforms agrees with the leading terms of the solution obtained by geometric optics when the latter is expanded in powers of small ϵ r.

The overall effect of the shear is to confine the wave field on the downstream side of the disturbance to a region which is smaller than the wave region in the case of uniform flows. If U(y) vanishes, and changes sign at a critical plane y = y_cr (e.g. ϵy_cr = -1 for the case of linear shear), then the boundary of this asymmetric wave field approaches this critical vertical plane. On this boundary the wave crests are all perpendicular to the x-axis, indicating that waves are reflected at this boundary.

Inside the wave field, as in the case of a point disturbance in a uniform primary flow, there exist two wave systems. The loci of constant phases (such as the crests or troughs) of these wave systems are not symmetric with respect to the x-axis. The geometric optics method and the integral transform method yield the same result of these loci for the special case of U(y) = U_o(1 + ϵy) and for large Kr (ϵr ˂˂ 1 ˂˂ Kr).

An expression for the variation of the amplitude of the waves in the wave field is obtained by the integral transform method. This is in the form of an expansion in small ϵr. The zeroth order is identical to the expression for the uniform stream case and is thus not applicable near the boundary of the wave region because it becomes infinite in that neighborhood. Throughout this investigation the viscous terms in the equations of motion are neglected, a reasonable assumption which can be justified when the wavelengths of the resulting waves are sufficiently large.

Wireless optical communication-based spatial pattern

We propose a novel communication technique which utilizes a set of mutually distinguishable optical patterns instead of convergent facula to transmit information. The communication capacity is increased by exploiting the optical spatial bandwidth resources. An optimum detector for this communication is proposed based on maximum-likelihood decision. The fundamental rule of designing signal spatial pattern is formulated from analysis of the probability of error decision. Finally, we present a typical electro-optical system scheme of the proposed communication. (c) 2006 Elsevier GmbH. All rights reserved.

Multi-channel 2-D pattern transfer model based on imaging optics for submarine laser uplink communication

An optical communication scheme of 2-D pattern transfer based on imaging optics for submarine laser uplink communication (SLUC) is suggested. Unlike the methods aiming at avoiding neighboring crosstalk used in traditional multi-channel optical beam transferring, we make full use of the overlapping of each spreading beam other than controlling divergence effect of each beam to avoid interference noise. The apparent parameters have been introduced to simplify theoretical analysis of optical pattern transfer problem involving underwater condition, with the help of which the complex beam propagation inside two kinds of mediums can be easily reduced to brief beam transfer only inside air medium. In this paper, optical transmission path and receiver terminal optics geometry have been described in detail. The link range equation and system uplink performance analysis have also been given. At last, results of a proof-of-concept experiment indicate good feasibility of the proposed SLUC model. © 2007 Elsevier GmbH. All rights reserved.

Smoothing the side lobes of a focused pattern by spectral dispersion in the broadband laser

Starting from the Huygens-Fresnel diffraction integral, the propagation equations of a broadband laser passing through a dispersive lens and a dispersive wedge are derived. Smoothing effect on the side lobes of the focused pattern is achieved as the broadband laser passes through the lens because of the spectral dispersion of the lens. By inserting a dispersive wedge behind the lens, better smoothing effect is realized because a relative position shift between focused patterns of different frequency components is generated due to the spectral dispersion of the wedge. Smoothing effect on the side lobe is obtained even with small bandwidth of the broadband laser as the wedge is used. (c) 2006 Elsevier GmbH. All rights reserved.

Bertso transformation with pattern-based sampling

This paper presents a method to generate new melodies, based on conserving the semiotic structure of a template piece. A pattern discovery algorithm is applied to a template piece to extract significant segments: those that are repeated and those that are transposed in the piece. Two strategies are combined to describe the semiotic coherence structure of the template piece: inter-segment coherence and intra-segment coherence. Once the structure is described it is used as a template for new musical content that is generated using a statistical model created from a corpus of bertso melodies and iteratively improved using a stochastic optimization method. Results show that the method presented here effectively describes a coherence structure of a piece by discovering repetition and transposition relations between segments, and also by representing the relations among notes within the segments. For bertso generation the method correctly conserves all intra and inter-segment coherence of the template, and the optimization method produces coherent generated melodies.

Análise molecular vibracional da interface adesivo-dentina após aplicação de múltiplas camadas de sistemas adesivos convencionais de dois passos

O propósito do presente estudo foi analisar o efeito da aplicação de múltiplas camadas consecutivas de dois sistemas adesivos convencionais de dois passos na difusão resinosa e padrão de distribuição dos componentes monoméricos resinosos. Dezesseis terceiros molares humanos hígidos foram tratados com os sistemas adesivos convencionais de dois passos de acordo com as instruções dos fabricantes ou com aplicações em múltiplas camadas consecutivas. Os espécimes foram seccionados paralelamente aos túbulos dentinários e as superfícies submetidas ao polimento com lixas 600, 1200, 1800, 2000 e 4000. Os espectros Raman foram coletados ao longo de uma linha perpendicular a interface adesivo-resina em intervalos de 1 ou 2 m. As medidas de difusão da resina adesiva e distribuição dos componentes monomériccos foram avaliadas pelos picos Raman de 1113 cm-1, 1609 cm-1 e 1454 cm-1. O gradiente de desmineralização usado na determinação da região de hibridização foi avaliado pelo pico de 960 cm-1 da apatita. De acordo com os resultados obtidos, a aplicação de múltiplas camadas apresentou uma tendência de homogeneização dos componentes poliméricos, dependente da composição química da resina adesiva.

Análise da tectônica de colocação de diques cretácicos na região de São Sebastião, SP

O trabalho foi desenvolvido no litoral norte do estado de São Paulo, onde ocorrem boas exposições de rochas intrusivas da porção meridional do Enxame de Diques da Serra do Mar, de idade eocretácica. O objetivo principal da dissertação é caracterizar os regimes tectônicos associados à colocação e à deformação de diques máficos na área de São Sebastião (SP) e sua distribuição espacial, a partir de interpretações de imagens de sensores remotos, análise de dados estruturais de campo e descrição petrográfica das rochas ígneas. A área apresenta grande complexidade no tocante ao magmatismo, uma vez que ocorrem diques de diabásios toleítico e alcalino, lamprófiro e rochas alcalinas félsicas como fonolitos, traquitos e sienitos, estes sob a forma diques, sills e plugs. Os diabásios toleíticos tem idades em torno 134 Ma, correlatas com o início do rifteamento sul-atlântico, enquanto que as rochas alcalinas datam de 86 Ma e estão relacionadas com um magmatismo intraplaca posterior. Os lineamentos estruturais orientam-se majoritariamente na direção ENE-WSW, paralela às foliações metamórficas e zonas de cisalhamento observadas no campo e descritas na literatura, referentes ao Domínio Costeiro da Faixa Ribeira. Os diques se orientam na direção NE-SW, com azimute semelhante porém ângulos de mergulho discordantes da foliação em grande parte da área, onde as foliações são de baixo ângulo. Um segundo conjunto de lineamentos orientado NW-SE ocorre como um importante conjunto de fraturas que cortam tanto as rochas do embasamento proterozóico quanto as rochas alcalinas neocretácicas. Diques com esta orientação são escassos. Um terceiro conjunto NNE-SSW ocorre na porção oeste da área, associado à presença de diques de diabásio que por vezes mostram indicadores de movimentação sinistral. A análise cinemática dos diques mostra um predomínio de distensão pura durante sua colocação, com um tensor de compressão mínima de orientação NW-SE, ortogonal ao principal trend dos diques. Componentes direcionais, por vezes ambíguas, são comumente observadas, com um discreto predomínio de componente sinistral. O mesmo padrão cinemático é observado para os diques toleíticos e para os alcalinos, sugerindo que o campo de tensões local pouco variou durante o Cretáceo. Embora o embasamento não tenha sido diretamente reativado durante a colocação dos diques, sua anisotropia pode ter controlado de certa forma a orientação do campo de tensões local durante o Cretáceo. Os mapas geofísicos da bacia de Santos existentes na literatura sugerem certo paralelismo entre as estruturas observadas na área de estudo e aquelas interpretadas na bacia. As estruturas NNE-SSW são paralelas ao trend das sub-bacias e ao gráben de Merluza, enquanto que as estruturas NW-SE são paralelas a zonas de transferência descritas na literatura.