Impact of carrier stiffness and microtopology on two-dimensional kinetics of P-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) interactions

Mechanics and surface microtopology of the molecular carrier influence cell adhesion, but the mechanisms underlying these effects are not well understood. We used a micropipette adhesion frequency assay to quantify how the carrier stiffness and microtopology affected two-dimensional kinetics of interacting adhesion molecules on two apposing surfaces. Interactions of P-selectin with P-selectin glycoprotein ligand-1 (PSGL-1) were used to demonstrate such effects by presenting the molecules on three carrier systems: human red blood cells (RBCs), human promyelocytic leukemia HL-60 cells, and polystyrene beads. Stiffening the carrier alone or in cooperation with roughing the surface lowered the two-dimensional affinity of interacting molecules by reducing the forward rate but not the reverse rate, whereas softening the carrier and roughing the surface had opposing effects in affecting two-dimensional kinetics. In contrast, the soluble antibody bound with similar three-dimensional affinity to surface-anchored P-selectin or PSGL-1 constructs regardless of carrier stiffness and microtopology. These results demonstrate that the carrier stiffness and microtopology of a receptor influences its rate of encountering and binding a surface ligand but does not subsequently affect the stability of binding. This provides new insights into understanding the rolling and tethering mechanism of leukocytes onto endothelium in both physiological and pathological processes.

Stratification by solid particle suspensions

Turbulence was generated by an oscillating grid above a bed of sediment of spherical glass beads. As expected, part of the sediment was lifted up by the grid action and a suspension layer of depth D formed above the grid. This depth was found remaining independent of grid action but varying with the sediment layer depth when the grid action was kept constant. Volume concentration measurements show the existence of only weak concentration gradients over the layer depth with a rapid fall off in concentration at the outer edge. The theoretical analysis based on a concentration flux model is in good qualitative agreement with observations.

Dissipative particle dynamics simulation of wettability alternation phenomena in the chemical flooding process

Wettability alternation phenomena is considered one of the most important enhanced oil recovery (EOR) mechanisms in the chemical flooding process and induced by the adsorption of surfactant on the rock surface. These phenomena are studied by a mesoscopic method named as dissipative particle dynamics (DPD). Both the alteration phenomena of water-wet to oil-wet and that of oil-wet to water-wet are simulated based on reasonable definition of interaction parameters between beads. The wetting hysteresis phenomenon and the process of oil-drops detachment from rock surfaces with different wettability are simulated by adding long-range external forces on the fluid particles. The simulation results show that, the oil drop is liable to spread on the oil-wetting surface and move in the form of liquid film flow, whereas it is likely to move as a whole on the water-wetting surface. There are the same phenomena occuring in wettability-alternated cases. The results also show that DPD method provides a feasible approach to the problems of seepage flow with physicochemical phenomena and can be used to study the mechanism of EOR of chemical flooding.

Numerical modeling of optical levitation and trapping of the "stuck" particles with a pulsed optical tweezers

We present the theoretical analysis and the numerical modeling of optical levitation and trapping of the stuck particles with a pulsed optical tweezers. In our model, a pulsed laser was used to generate a large gradient force within a short duration that overcame the adhesive interaction between the stuck particles and the surface; and then a low power continuous - wave (cw) laser was used to capture the levitated particle. We describe the gradient force generated by the pulsed optical tweezers and model the binding interaction between the stuck beads and glass surface by the dominative van der Waals force with a randomly distributed binding strength. We numerically calculate the single pulse levitation efficiency for polystyrene beads as the function of the pulse energy, the axial displacement from the surface to the pulsed laser focus and the pulse duration. The result of our numerical modeling is qualitatively consistent with the experimental result. (C) 2005 Optical Society of America.

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.

Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics

The first chapter of this thesis deals with automating data gathering for single cell microfluidic tests. The programs developed saved significant amounts of time with no loss in accuracy. The technology from this chapter was applied to experiments in both Chapters 4 and 5.

The second chapter describes the use of statistical learning to prognose if an anti-angiogenic drug (Bevacizumab) would successfully treat a glioblastoma multiforme tumor. This was conducted by first measuring protein levels from 92 blood samples using the DNA-encoded antibody library platform. This allowed the measure of 35 different proteins per sample, with comparable sensitivity to ELISA. Two statistical learning models were developed in order to predict whether the treatment would succeed. The first, logistic regression, predicted with 85% accuracy and an AUC of 0.901 using a five protein panel. These five proteins were statistically significant predictors and gave insight into the mechanism behind anti-angiogenic success/failure. The second model, an ensemble model of logistic regression, kNN, and random forest, predicted with a slightly higher accuracy of 87%.

The third chapter details the development of a photocleavable conjugate that multiplexed cell surface detection in microfluidic devices. The method successfully detected streptavidin on coated beads with 92% positive predictive rate. Furthermore, chambers with 0, 1, 2, and 3+ beads were statistically distinguishable. The method was then used to detect CD3 on Jurkat T cells, yielding a positive predictive rate of 49% and false positive rate of 0%.

The fourth chapter talks about the use of measuring T cell polyfunctionality in order to predict whether a patient will succeed an adoptive T cells transfer therapy. In 15 patients, we measured 10 proteins from individual T cells (~300 cells per patient). The polyfunctional strength index was calculated, which was then correlated with the patient's progress free survival (PFS) time. 52 other parameters measured in the single cell test were correlated with the PFS. No statistical correlator has been determined, however, and more data is necessary to reach a conclusion.

Finally, the fifth chapter talks about the interactions between T cells and how that affects their protein secretion. It was observed that T cells in direct contact selectively enhance their protein secretion, in some cases by over 5 fold. This occurred for Granzyme B, Perforin, CCL4, TNFa, and IFNg. IL- 10 was shown to decrease slightly upon contact. This phenomenon held true for T cells from all patients tested (n=8). Using single cell data, the theoretical protein secretion frequency was calculated for two cells and then compared to the observed rate of secretion for both two cells not in contact, and two cells in contact. In over 90% of cases, the theoretical protein secretion rate matched that of two cells not in contact.

The rate and mechanism of the partial oxidation of acetaldehyde by PPM concentrations of nitrogen dioxide

The thermal reaction between nitrogen dioxide and acetaldehyde in the gas phase was investigated at room temperature and atmospheric pressure. The initial rate of disappearance of nitrogen dioxide was 1.00 ± 0.03 order with respect to nitrogen dioxide and 1.00 ± 0.07 order with respect to acetaldehyde. An initial second order rate constant of (8.596 ± 0.189) x 10^-3 1.mole^-1 sec^-1 was obtained at 22.0 ± 0.1 °C and a total pressure of one atmosphere. The activation energy of the reaction was 12,900 cal/mole in the temperature range between 22°C and 122°C.

The products of the reaction were nitric oxide, carbon dioxide, methyl nitrite, nitromethane and a trace amount of trans-dimeric nitrosomethane. The addition of nitric oxide increased the rate of formation of nitromethane and decreased the rate of formation of methyl nitrite. There were no measurable surface effects due to the addition of glass wool or glass beads to the reactor.

Reactants and products were analyzed by gas chromatography. A mechanism was proposed incorporating the principal features of the reaction.

一批中国古玻璃化学成分的质子激发X射线荧光分析

质子激发X射线荧光(proton induced X-ray emission，PIXE)技术是一种高灵敏度、非破坏性、多元素定量测定的分析方法。采用外束PIXE技术对内蒙古地区和博山出土的一批古代玻璃的化学成分进行了定量测定。结果表明：内蒙古地区出土的玻璃中，西周时期的玻璃珠是含有少量K2O和CaO助熔剂的釉砂，其主要成分为SiO2；汉代的玻璃珠属于PbO—SiO2玻璃；多数元代的玻璃制品和部分北魏时期的玻璃珠属于K2O—CaO—SiO2玻璃。博山出土的元末明初的玻璃基本为KzO-CaO—SiO2系玻璃

一批中国古代镶嵌玻璃珠化学成分的检测报告

结合外束质子激发X荧光（proton induced X-ray emission,PIXE）和能量色散X射线荧光（energy dispersive X-ray emission,EDXRF）分析技术,对中国新疆、湖北、四川、广东出土的古代镶嵌玻璃珠的化学成分进行了检测.结果表明：新疆拜城克孜尔墓地出土的西周-春秋时期镶嵌玻璃珠为CaO-MgO-SiO2玻璃,战国时期中国境内的PbO-BaO-SiO2和Na2O-CaO-SiO2镶嵌玻璃珠是同时存在的.本文亦对相关问题进行了一些讨论,并提出了部分今后的工

四川地区出土古玻璃的质子激发X荧光分析

abstract {Proton induced X-ray emission (PIXE) technique is an effective method for the chemical composition analysis of ancient glass samples without destruction. Chemical composition of the ancient glass samples dated from the Warring States Period (770-476 B.C.) to the Six Dynasties Period (220-589 A.D.), which were unearthed in Sichuan area, was quantitatively determined by the PIXE technique. The results show that the glass Bi (disc) and the glass eye beads of the Warring States Period all belong to the PbO-BaO-SiO₂ system. According to the composition and shape, we infer that these glass Bi and eye beads were made in China. Whereas, the chemical compositions of the glass ear pendants and beads of the Six Dynasties Period are varied, including K₂O-CaO-SiO₂, K₂O-SiO₂ and other glass systems. Based on the obtained results and those from literatures, some questions related to the technical propagation of the ancient Chinese glass are discussed.}

Data Gathering Bias: Trait Vulnerability to Psychotic Symptoms?

Background Jumping to conclusions (JTC) is associated with psychotic disorder and psychotic symptoms. If JTC represents a trait, the rate should be (i) increased in people with elevated levels of psychosis proneness such as individuals diagnosed with borderline personality disorder (BPD), and (ii) show a degree of stability over time. Methods The JTC rate was examined in 3 groups: patients with first episode psychosis (FEP), BPD patients and controls, using the Beads Task. PANSS, SIS-R and CAPE scales were used to assess positive psychotic symptoms. Four WAIS III subtests were used to assess IQ. Results A total of 61 FEP, 26 BPD and 150 controls were evaluated. 29 FEP were revaluated after one year. 44% of FEP (OR = 8.4, 95% CI: 3.9-17.9) displayed a JTC reasoning bias versus 19% of BPD (OR = 2.5, 95% CI: 0.8-7.8) and 9% of controls. JTC was not associated with level of psychotic symptoms or specifically delusionality across the different groups. Differences between FEP and controls were independent of sex, educational level, cannabis use and IQ. After one year, 47.8% of FEP with JTC at baseline again displayed JTC. Conclusions JTC in part reflects trait vulnerability to develop disorders with expression of psychotic symptoms.

Interações do cobre iônico com microalgas verdes

No presente trabalho foram utilizados micro-organismos fotoautotróficos para a bioacumulação de cobre em regime de batelada. Para tal, utilizou-se micro-organismos dos gêneros Ankistrodesmus, Golenkinia, Monoraphidium e Scenedesmus, em função da sua disponibilidade, facilidade de cultivo e diferenças morfológicas. Ensaios preliminares foram realizados utilizando diferentes concentrações de biossorvente, com o intuito de verificar a influência deste fator na eficiência do processo de captação. Os testes realizados em batelada incluíram também o estudo cinético e do equilíbrio, nos quais foi possível verificar que para todos os gêneros testados, o processo de captação do metal em soluções diluídas atingiu o equilíbrio quase instantaneamente. Em soluções de Cu2+ mais concentradas, observou-se diferenças entre os gêneros estudados, no tempo necessário para estabelecimento do equilíbrio. Além disso, observou-se uma alta eficiência no processo de captação de íons Cu2+ em solução por parte dos micro-organismos, com elevada captação de metal por grama de biomassa. As diferenças morfológicas entre os gêneros pareceram não influenciar significativamente a cinética e o equilíbrio do processo. Os ensaios em batelada foram realizados também empregando-se células de Golenkinia imobilizadas em alginato de cálcio, além de testes com o próprio alginato isento de micro-organismos como experimento-controle afim de verificar a influencia da imobilização nos parâmetros cinéticos e na capacidade de captação. A partir dos resultados obtidos nos ensaios em batelada com todos os biossorventes, testou-se em cada caso a aplicação de modelos cinéticos (pseudo 1 e 2 ordem) e modelos de equilíbrio (isoterma de Langmuir e Freundlich). Verificou-se que para o 4 gêneros que empregando-se células livres o modelo cujo os resultados se adequaram melhor foi o de Langmuir, enquanto que para células imobilizadas ambos modelos se mostraram adequados

Electroosmotic flow analysis of a branched U-turn nanofluidic device.

In this paper, we present the analysis of electroosmotic flow in a branched -turn nanofluidic device, which we developed for detection and sorting of single molecules. The device, where the channel depth is only 150 nm, is designed to optically detect fluorescence from a volume as small as 270 attolitres (al) with a common wide-field fluorescent setup. We use distilled water as the liquid, in which we dilute 110 nm fluorescent beads employed as tracer-particles. Quantitative imaging is used to characterize the pathlines and velocity distribution of the electroosmotic flow in the device. Due to the device's complex geometry, the electroosmotic flow cannot be solved analytically. Therefore we use numerical flow simulation to model our device. Our results show that the deviation between measured and simulated data can be explained by the measured Brownian motion of the tracer-particles, which was not incorporated in the simulation.

Culture of pearl in freshwater mussels (Lamellidens marginalis Lamarck)

A pond trail on pearl culture in freshwater mussels, Lamellidens marginalis was carried out for one year in an artificial perennial pond. Four types of foreign particles of indigenous sources, sand, stone, fish eyeball and beads of artificial pearl nucleus were used as nucleus for pearl production. Among the nuclei inserted mussel highest survival rate (72%) was recorded for stone and lowest survival rate (50%) for artificial pearl by nucleus implantation. Highest pearl production rate (%) was recorded for the insertion of stone and lowest for the sand. All nuclei inserted mussel produced pearl accept the mussel which was inserted beads of pearl nucleus for pearl formation. Growth rate (length and weight) was found higher for uninserted mussel than nuclei inserted mussels.

Transitions in the erosive wear behavior of a glass-ceramic

The mechanisms of material removal were investigated during the erosive wear of a glass-ceramic. The effects of erodent particle shape, velocity and angle were studied. Single impacts and incremental erosion tests were performed, to study the development of surface features and to elucidate the mechanisms of material removal. It was found that transitions in mechanism occurred which depended on the particle shape, impact velocity and impact angle. The mechanisms of material removal, for erosion by silica sand, changed from fine scale fracture and plastic processes below a transition point to large-scale cracking of the surface above. Spherical glass beads caused wear dominated by fatigue, with a very strong dependence of wear rate on the impact conditions. This work indicates that laboratory erosion testing of glass-ceramic and other brittle materials should reflect the conditions present in practice, and that account must be taken of possible changes in wear mechanisms.