Proteomic analysis reveals platelet factor 4 and beta-thromboglobulin as prognostic markers in severe acute respiratory syndrome

Previously, we reported that proteomic fingerprints were present in sera of patients with severe acute respiratory syndrome (SARS), and could separate patients into subgroups with different prognoses. In the present study, we examined the prognostic values of the SARS-associated proteomic features by biostatistical analysis, and deciphered the identities of those with prognostic values. Data of 20 SARS-associated serum proteomic features and ten serological variables from 38 SARS adult patients before treatment were subjected to multivariate logistic regression. Proteomic features of m/z 6634, m/z 7769, m/z 8635, and m/z 8865 were identified as independent prognostic markers. After purification by cation-exchange chromatography and gel electrophoresis, proteomic features of m/z 7769 and m/z 8865 were found to be platelet factor 4 (PF4) and beta-thromboglobulin (beta-TG) by tandem mass spectrometry, respectively. The associations of decreased serum PF4 and increased serum beta-TG levels with poor prognosis were confirmed by Western blot. Previous studies suggest that PF4 and beta-TG are involved in the pathogenesis of acute respiratory distress syndrome (ARDS) in a negative and positive way, respectively. Our results suggest that PF4 and beta-TG may also play similar roles in the development of ARDS in SARS patients.     

Structural study of DNA condensation induced by novel phosphorylcholine-based copolymers for gene delivery and relevance to DNA protection

Poly[2-(dimethylamino)ethyl methacrylate-b-2-methacryloyloxyethyl phosphorylcholine] (DMA-MPC) is currently under investigation as a new vector candidate for gene therapy. The DMA block has been previously demonstrated to condense DNA effectively. The MPC block contains a phosphorylcholine (PC) headgroup, which can be found naturally in the outside of the cell membrane. This PC-based polymer is extremely hydrophilic and acts as a biocompatible steric stabilizer. In this study, we assess in detail the morphologies of DNA complexes obtained using the diblock copolymer series DMA(x)MPC30 (where the mean degree of polymerization of the MPC block was fixed at 30 and the DMA block length was systematically varied) using transmission electron microscopy (TEM) and liquid atomic force microscopy (AFM). Both techniques indicate more compact complex morphologies (more efficient condensation) as the length of the cationic DMA block increases. However, the detailed morphologies of the DMA(x)MPC30-DNA complexes observed by TEM in vacuo and by AFM in aqueous medium are different. This phenomena is believed to be related to the highly hydrophilic nature of the MPC block. TEM studies revealed that the morphology of the complexes changes from loosely condensed structures to highly condensed rods, toroids, and oval-shaped particles as the DMA moiety increases. In contrast, morphological changes from plectonemic loops to flower-like and rectangular block-like structures, with an increase in highly condensed central regions, are observed by in situ AFM studies. The relative population of each structure is clearly dependent on the polymer molecular composition. Enzymatic degradation assays revealed that only the DMA homopolymer provided effective DNA protection against DNase I degradation, while other highly condensed copolymer complexes, as judged from TEM and gel electrophoresis, only partially protected the DNA. However, AFM images indicated that the same highly condensed complexes have less condensed regions, which we believe to be the initiation sites for enzymatic attack. This indicates that the open structures observed by AFM of the DNA complexation by the DMA(x)MPC30 copolymer series are closer to in vivo morphology when compared to TEM.     

Aqueous fraction of Nephelium ramboutan-ake rind induces mitochondrial-mediated apoptosis in HT-29 human colorectal adenocarcinoma cells

The aim of this study was to investigate the cytotoxic and apoptotic effects of Nephelium ramboutan-ake (pulasan) rind in selected human cancer cell lines. The crude ethanol extract and fractions (ethyl acetate and aqueous) of N. ramboutan-ake inhibited the growth of HT-29, HCT-116, MDA-MB-231, Ca Ski cells according to MTT assays. The N. ramboutan-ake aqueous fraction (NRAF) was found to exert the greatest cytotoxic effect against HT-29 in a dose-dependent manner. Evidence of apoptotic cell death was revealed by features such as chromatin condensation, nuclear fragmentation and apoptotic body formation. The result from a TUNEL assay strongly suggested that NRAF brings about DNA fragmentation in HT-29 cells. Phosphatidylserine (PS) externalization on the outer leaflet of plasma membranes was detected with annexin V-FITC/PI binding, confirming the early stage of apoptosis. The mitochondrial permeability transition is an important step in the induction of cellular apoptosis, and the results clearly suggested that NRAF led to collapse of mitochondrial transmembrane potential in HT-29 cells. This attenuation of mitochondrial membrane potential (Δψm) was accompanied by increased production of ROS and depletion of GSH, an increase of Bax protein expression, and induced-activation of caspase-3/7 and caspase-9. These combined results suggest that NRAF induces mitochondrial-mediated apoptosis.     

Cross-polarization dynamics in polycrystalline samples

We observe non-monotonic development of the ¹³C magnetization in polycrystalline samples of glycine, sucrose, and adamantine during cross-polarization. We demonstrate, by fitting the time dependence, that the development quantitatively results from dipolar oscillations. To fit the data quantitatively requires one to assume two types of spin-diffusion behavior.     

Interpretation of chromatographic retentions of simple solutes with an amylose-based sorbent using infrared spectroscopy and DFT modeling

The interactions of amylose tris(3,5-dime- thylphenylcarbamate) (ADMPC, commercially “Chiralpak AD”) with 10 simple solutes—1-propanol, heptane, heptanol, benzene, propylbenzene, benzyl alcohol, pyridine, tetrahydrofuran, diethylamine, and aniline—are studied using attenuated total reflection infrared spectroscopy (ATR-IR) of thin polymer films, DFT modeling, and high performance liquid chromatography (HPLC). ATR-IR is used to determine the changes in the hydrogen bonding states of the C=O and NH groups of the polymer amide I and II bands upon absorption of each of the solutes at 25^∘C. DFT modeling with B3LYP/6-311+g(d,p) level of theory is used to predict the IR wavenumbers, the H-bonding interaction energies, and the hydrogen bonding distances of the polymer side-chains with certain solute molecules. The capacity factors of these solutes with ADMPC have been measured at 25^∘C in hexane/isopropanol (95/5, v/v) solvent. From IR data and DFT modeling, we conclude that the C=O and NH are key binding sites of the polymer and interact with the functional groups of various solutes. The capacity factors are understood on the basis of hydrogen bonding, hydrophobic, and dipole-dipole interactions of the C=O, NH, and phenyl groups of the sorbent with OH, NH, NH₂, O, phenyl, and N functional groups of the solutes.     

Scanning tunnelling microscopy imaging and modification of hydrogen-passivated Ge(100) surfaces

Scanning tunnelling microscopy (STM) study and modification of hydrogen (H)-passivated Ge(100) surfaces have been investigated. Thermal oxidation procedures were used to minimise surface roughness. Ge samples were passivated in HF solution after thermal oxidation. STM and atomic force microscope (AFM) imaging showed that, using HF etching after thermal oxidation, we can obtain a natural H-passivatedtopographically and chemically flat Ge(100) surface. The root-mean-square (rms) roughness ofa H-passivatedGe(100) surface measured both by STM and AFM is less than 2 ?. Electric properties of H-passivatedGe(100) surfaces were studied by scanning tunnelling spectroscopy (STS) in nitrogen ambient. STS showed that the H-passivated Ge surfaces were not pinned. Modification on H-passivated Ge(100) surfaces was carried out using STM by applying an electric voltage between the sample and tip in air. Modified features were characterised by STM and AFM imaging. On the H-passivated Ge(100) surfaces, stable, low-voltage, nanometer-scale modified features can be produced.     

In situ probing of insulin aggregation in chromatography effluents with spectroturbidimetry

Probing protein aggregation in situ is quite important for analyzing and developing chromatographic protein purification processes. A spectroturbidimetry method with a photodiode array detector is developed and tested for probing insulin aggregation in solution and determining the aggregation number, n(m). All aggregates examined are in the Rayleigh light scattering regime, where the turbidity between 400 and 350 nm is proportional to lambda(-4). Insulin at 25 degrees C in 3.5 N acetic acid is mainly monomeric (non-aggregated). At 25 degrees C and lower acetic acid concentrations, from 0.1 to 1 N, the average insulin aggregation number n(m) ranges from 2.9 to 1.6. Aggregates, with n(m) = 2-3, are found in 2.6 N acetic acid with 20 vol% acetonitrile. In 0.8 N acetic acid with 20 vol% denatured ethanol, n(m) = 1.2. At 4 degrees C, as acetic acid concentration decreases from 3.5 to 0.1 N, n(m) decreases from 2.4 to 1.8. In 2.8 N acetic acid with 20 vol% denatured ethanol at 4 degrees C, insulin exists mainly in monomer form. In situ probing of size exclusion chromatography, SEC, effluents in 3.5 N acetic acid at 4 degrees C shows n(m) = 1.6 at the fronting portion (a mixture of monomers and dimers or other oligomers) and n(m) = 1.1 (mostly monomers) at the tailing portion of the main peak. In another example, for LysPro-insulin in reversed phase chromatography at 4 degrees C, complex elution patterns and broad peaks are due to substantial aggregation. For a linear gradient of acetonitrile from 10 to 60 vol% at 4 degrees C, n(m) ranges from 2.2 to 12, in order of elution. For a linear gradient of ethanol from 30 to 50 vol% at 4 degrees C, n(m) ranges from 14 to 27, in order of elution. Analytical HPLC results at 25 degrees C imply that the aggregates are reversible.     

Interfacial-layer-free growth of yttrium oxide on germanium by understanding initial surface reactions

In this study, we investigate the surface and interfacial reactions involved in the growth of yttrium oxide through the oxidation of yttrium metal on germanium. Our combined understanding of the oxidation and interfacial reactions allows us to introduce a layer-by-layer method to grow an interfacial-layer-free yttrium oxide on germanium at room temperature, which has previously proven to be difficult. During initial growth, we show evidence that yttrium germanide provides the lowest kinetic pathway in the formation of the yttrium germanate interfacial layer and explain how this pathway can be avoided using our layer-by-layer method. This method can possibly be used to achieve interfacial-layer-free growth for other metal oxides on semiconductors.     

First‐principles study on the concentrations of native point defects in high‐dielectric‐constant binary oxide materials

The intrinsic concentrations of point defects in high‐k binary oxide materials of HfO₂, ZrO₂, Y₂O₃ and La₂O₃ are evaluated on the basis of first‐principles calculations. Oxygen defects are found to dominate over a wide range of the oxygen chemical potential. Neutral oxygen vacancies are likely to be responsible for electron trapping in the investigated materials. In HfO₂ and ZrO₂, oxygen Frenkel pairs are likely to form. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)