Characterization of iodine species in the marine aerosol: To understand their roles in particle formation processes

In this contribution, iodine chemistry in the Marine Boundary Layer (MBL) is introduced. A series of methodologies for the measurements of iodine species in the gas and particle phases of the coastal atmosphere has been developed. Iodine species in the gas phase in real air samples has been determined in two field campaigns at the west coast of Ireland, indicating that gaseous iodo-hydrocarbons and elemental iodine are the precursors of new particle formation. Particulate iodine speciation from the same measurement campaigns show that the non-water-soluble iodine compounds are the main iodine species during the marine particle formation. A seaweed-chamber experiment was performed, indicating that gaseous I₂ is one of the important precursors that lead to new particle formation in the presence of solar light in the ambient air at the coastal tidal area.     

Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-pi interactions

At the interface between protein and double-stranded DNA, stair motifs simultaneously involve three different types of pairwise interactions: aromatic base stacking, hydrogen bonding, and cation-pi. The relative importance of these interactions is studied in the stair motif occurring in the 1TC3 crystal structure, which involves an arginine and two stacked guanines, by means of Hartree-Fock (HF) and M?ller-Plesset energy and free energy calculations, including vibrational, rotational, translational contributions, both in a vacuum and various solvents. The results obtained show an anti-cooperative tendency of the HF energy and vibrational free energy terms, and the cooperativity of the rotational, translational, and solvation free energies. Hence, the cooperativity of the stair motif interactions, in the context of protein-DNA recognition, can be viewed as arising from the environment.     

亲和毛细管电泳技术在蛋白质-DNA相互作用研究中的应用

蛋白质-DNA的相互作用在决定细胞命运的许多过程中发挥重要作用,对蛋白质-DNA相互作用的分子机制研究有利于对基本生命过程的理解,为相关疾病的临床治疗及药物筛选提供理论指导。另一方面,利用一些已知的蛋白质-DNA相互作用可以帮助开发先进的生物工程和生命分析技术,为相关研究提供有力的技术支持。因此,建立灵敏、快速的分析方法用于表征蛋白质-DNA的相互作用十分重要。高效毛细管电泳(capillary electrophoresis, CE)技术因其超高的分离效率、极低的样品消耗与较短的分析时间等优势被广泛应用于化学、生命科学和环境科学等多个研究领域。其中,亲和毛细管电泳(affinity capillary electrophoresis, ACE)技术已经成为考察分子间相互作用的重要研究工具。这篇文章综述了亲和毛细管电泳技术自建立以来在蛋白质-DNA相互作用分析方面的研究进展,并对经典的研究工作进行了着重介绍,主要包括三方面的内容:(1)亲和毛细管电泳技术简介;(2)利用亲和毛细管电泳技术进行蛋白质-DNA相互作用的基础分子机制研究;(3)利用已知的蛋白质-DNA相互作用发展针对目标分子...     

The laser-induced blue state of bacteriorhodopsin: mechanistic and color regulatory roles of protein-protein interactions, protein-lipid interactions, and metal ions

In this paper we characterize the mechanistic roles of the crystalline purple membrane (PM) lattice, the earliest bacteriorhodopsin (BR) photocycle intermediates, and divalent cations in the conversion of PM to laser-induced blue membrane (LIBM; lambda(max)= 605 nm) upon irradiation with intense 532 nm pulses by contrasting the photoconversion of PM with that of monomeric BR solubilized in reduced Triton X-100 detergent. Monomeric BR forms a previously unreported colorless monomer photoproduct which lacks a chromophore band in the visible region but manifests a new band centered near 360 nm similar to the 360 nm band in LIBM. The 360 nm band in both LIBM and colorless monomer originates from a Schiff base-reduced retinyl chromophore which remains covalently linked to bacterioopsin. Both the PM-->LIBM and monomer-->colorless monomer photoconversions are mediated by similar biphotonic mechanisms, indicating that the photochemistry is localized within single BR monomers and is not influenced by BR-BR interactions. The excessively large two-photon absorptivities (> or =10(6) cm(4) s molecule(-1) photon(-1)) of these photoconversions, the temporal and spectral characteristics of pulses which generate LIBM in high yield, and an action spectrum for the PM-->LIBM photoconversion all indicate that the PM-->LIBM and Mon-->CMon photoconversions are both mediated by a sequential biphotonic mechanism in which is the intermediate which absorbs the second photon. The purple-->blue color change results from subsequent conformational perturbations of the PM lattice which induce the removal of Ca(2+) and Mg(2+) ions from the PM surface.     

Pervaporation from a dense membrane: roles of permeant-membrane interactions, Kelvin effect, and membrane swelling

Dense polymeric membranes with extremely small pores in the form of free volume are used widely in the pervaporative separation of liquid mixtures. The membrane permeation of a component followed by its vaporization on the opposite face is governed by the solubility and downstream pressure. We measured the evaporative flux of pure methanol and 2-propanol using dense membranes with different free volumes and different affinities (wettabilities and solubilities) for the permeant. Interestingly, the evaporative flux for different membranes vanished substantially (10-75%) below the equilibrium vapor pressure in the bulk. The discrepancy was larger for a smaller pore size and for more wettable membranes (higher positive spreading coefficients). This observation, which cannot be explained by the existing (mostly solution-diffusion type) models ofpervaporation, suggests an important role for the membrane-permeant interactions in nanopores that can lower the equilibrium vapor pressure. The pore sizes, as estimated from the positron annihilation, ranged from 0.2 to 0.6 nm for the dry membranes. Solubilities of methanol in different composite membranes were estimated from the Flory-Huggins theory. The interaction parameter was obtained from the surface properties measured by the contact angle goniometry in conjunction with the acid-base theory of polar surface interactions. For the membranes examined, the increase in the "wet" pore volume due to membrane swelling correlates almost linearly with the solubility of methanol in these membranes. Indeed, the observations are found to be consistent with the lowering of the equilibrium vapor pressure on the basis of the Kelvin equation. Thus, a higher solubility or selectivity of a membrane also implies stronger permeant-membrane interactions and a greater retention of the permeant by the membrane, thus decreasing its evaporative flux. This observation has important implications for the interpretation of existing experiments and in the separation of liquid mixtures by pervaporation.     

A general and rapid cell-free approach for the interrogation of protein-protein, protein-DNA, and protein-RNA interactions and their antagonists utilizing split-protein reporters

Split-protein reporters have emerged as a powerful methodology for imaging biomolecular interactions which are of much interest as targets for chemical intervention. Herein we describe a systematic evaluation of split-proteins, specifically the green fluorescent protein, beta-lactamase, and several luciferases, for their ability to function as reporters in completely cell-free systems to allow for the extremely rapid and sensitive determination of a wide range of biomolecular interactions without the requirement for laborious transfection, cell culture, or protein purification (12-48 h). We demonstrate that the cell-free split-luciferase system in particular is amenable for directly interrogating protein-protein, protein-DNA, and protein-RNA interactions in homogeneous assays with very high sensitivity (22-1800 fold) starting from the corresponding mRNA or DNA. Importantly, we show that the cell-free system allows for the rapid (2 h) identification of target-site specificity for protein-nucleic acid interactions and in evaluating antagonists of protein-protein and protein-peptide complexes circumventing protein purification bottlenecks. Moreover, we show that the cell-free split-protein system is adaptable for analysis of both protein-protein and protein-nucleic acid interactions in artificial cell systems comprising water-in-oil emulsions. Thus, this study provides a general and enabling methodology for the rapid interrogation of a wide variety of biomolecular interactions and their antagonists without the limitations imposed by current in vitro and in vivo approaches.     

Interplay between electrochemistry and optical imaging: The whole is greater than the sum of the parts

Optical techniques can afford a powerful characterisation of the solid–liquid interface that is composed of an electrode immersed in an electrolyte. While a typical electrochemical measurement such as current intensity is averaged over the entire electrode surface, the access to surface heterogeneity can provide an increased level of information enabling to rationalise and optimise the performance of chemical or biochemical sensors. In this opinion article, we will briefly review the different strategies developed to translate an electrochemical process into a luminescence signal. Also, several key examples will be selected and commented in order to highlight the key advantages of coupling electrochemistry with optical imaging, essentially fluorescence and electrochemiluminescence.     

The whole is more than the sum of its parts: Modeling community-level effects of UVR in marine ecosystems

The effect of UVB radiation (UVBR, 290-320 nm) on the dynamics of the lower levels of the marine plankton community was modeled. The model was built using differential equations and shows a good fit to experimental data collected in mesocosms (defined as large enclosures of 1500 L filled with natural marine waters). Some unexpected results appear to be possible by indirect effects in prey (bacteria, phytoplankton and heterotrophic flagellates). In particular, apparent competition appears between small phytoplankton and bacteria. This effect is caused by a shared predator (ciliates). Another remarkable effect is an increase in bacteria and flagellates populations due to enhanced UVBR. This effect is similar to that observed under mesocosm experimental conditions and is related to the decrease of predation due to the direct damage to predators (ciliates) by UVBR. The effect of UVBR changing interaction coefficients may be dramatic on the community structure, producing big changes in equilibrium populations, as demonstrated by sensitivity analysis of the model. In order to generalize these results to field conditions it will be necessary to increase model complexity and include extra organic mater sources, mixing and sinking effects and predation by large zooplankton. This work shows that UVBR may produce community global responses that are consequence of both direct and indirect effects among populations.     

Electrostatic interactions between double layers: influence of surface roughness, regulation, and chemical heterogeneities

Electrostatic interactions between two surfaces as measured by atomic force microscopy (AFM) are usually analyzed in terms of DLVO theory. The discrepancies often observed between the experimental and theoretical behavior are usually ascribed to the occurrence of chemical regulation processes and/or to the presence of surface chemical or morphological heterogeneities (roughness). In this paper, a two-gradient mean-field lattice analysis is elaborated to quantifying double layer interactions between nonplanar surfaces. It allows for the implementation of the aforementioned sources of deviation from DLVO predictions. Two types of ion-surface interaction ensure the adjustment of charges and potentials upon double layer overlap, i.e., specific ionic adsorption at the surfaces and/or the presence of charge-determining ions for the surfaces considered. Upon double layer overlap, charges and potentials are adjusted via reequilibrium of the different ion adsorption processes. Roughness is modeled by grafting asperities on supporting planar surfaces, with their respective positions, shapes, and chemical properties being assigned at will. Local potential and charge distributions are derived by numerically solving the nonlinear Poisson-Boltzmann equation under the boundary conditions imposed by the surface profiles and regulation mechanism chosen. Finite size of the ions is taken into account. A number of characteristic situations are briefly discussed. It is shown how the surface irregularities are reflected in the Gibbs energy of interaction.     

Activation of orotidine 5'-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts

We report that the binding of phosphite dianion to orotidine 5'-monophosphate decarboxylase (OMPDC) results in an 80 000-fold increase in kcat/Km for decarboxylation of the truncated substrate, 1-(beta-d-erythrofuranosyl)orotic acid (EO), which lacks a 5'-phosphodianion moiety. The intrinsic binding energy (IBE) of phosphite dianion in the transition state is 7.8 kcal/mol, which represents a very large fraction of the 11.8 kcal/mol IBE of the phosphodianion group of the natural substrate orotidine 5'-monophosphate (OMP). The data give kcat = 160 +/- 70 s-1 for turnover of EO in the active site of OMPDC containing phosphite dianion, which is significantly larger than kcat = 15 s-1 for turnover of OMP. Despite the weaker binding of the individual EO and HPO32- "parts" (KmKd = 0.014 M2) than of OMP (Km = 1.6 x 10-6 M), once bound, OMPDC provides a slightly greater stabilization of the transition state for reaction of the parts than of the whole substrate. Thus, the covalent connection between the reacting portion of the substrate and the nonreacting phosphodianion group is not necessary for efficient catalysis. This implies that a major role of the phosphodianion group of OMP is to provide binding interactions that are used to drive an enzyme conformational change, resulting in formation of an active site environment optimized for transition state stabilization.     

From whole body to molecule: an integrated approach to the regulation of metabolism and growth

This paper considers the use of whole-body calorimetry in a wide context, as one of a range of techniques available for advancing our knowledge of the regulation of energy metabolism and growth. This integrated approach should lead to a greater depth of understanding by investigating the mechanisms by which responses of the whole animal depend on events at the tissue, cellular and molecular levels.

Two critical stages of mammalian development, the perinatal and early postnatal periods, are discussed. Particular attention is paid to skeletal muscle and the extent to which myofibre differentiation and hypertrophy, and hence muscle function and energetic efficiency, can be modified by nutrition and the thermal environment. In view of the crucial roles of thyroid hormones, growth hormone and insulin-like growth factor-I in regulation of metabolism and growth, the role of the endocrine system is also considered. These studies have important implications for survival and optimal health of humans and other animals.     

Experimental and computational studies of the recognition of amino acids by galactosyl-imine and -amine derivatives: an attempt to understand the lectin-carbohydrate interactions

A galactosyl-naphthyl-imine-based derivative, 1-(beta-D-galactopyranosyl-1'-deoxy-1'-iminomethyl)-2-hydroxynaphthalene (GNI), and a galactosyl-naphthyl-amine-based derivative, 1-(galactopyranosyl-1'-deoxy-1'-aminomethyl)-2-hydroxynaphthalene (GNA), possessing an ONO binding core were studied for their recognition of naturally occurring amino acids using fluorescence and absorption spectroscopy, and the corresponding association constants were derived for the complexes formed. The complexes formed between GNI/GNA and amino acids were supported by electrospray ionization mass spectrometry (ESI/MS). The structures of the complexes were optimized by computational studies using density functional theory, and stabilization energies were computed for the complexes to substantiate the interactions present between GNI/GNA and amino acid. The interactions were found to be primarily hydrogen bonding in nature. These interactions are reminiscent of those present in the lectin-carbohydrate and glycosidase substrate. Thus, the carbohydrate moiety present in GNI shows high specificity toward the -COOH group of the amino acid, which may be relevant to such interactions present between the carbohydrates and the polypeptides.     

Self-assembled trimer structures highlight the competitive roles of intermolecular and adsorbate-substrate interactions: PVBA trimer on Pd(111)

We observed the orientation of 4-trans-2-(pyrid-4-yl-vinyl)benzoic acid (PVBA) trimers on Pd(111) using scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV). The image showed three different types of trimers, one of which does not follow predicted dimer orientations. This type of trimer displays 10° rotations of each molecule in clockwise or counterclockwise directions. Calculations of adsorbate-substrate energy and hydrogen bonding energy revealed that the rotations are a result of competition between adsorbate-adsorbate and adsorbate-substrate interactions.     

The flash-quench technique in protein-DNA electron transfer: reduction of the guanine radical by ferrocytochrome c

Electron transfer from a protein to oxidatively damaged DNA, specifically from ferrocytochrome c to the guanine radical, was examined using the flash-quench technique. Ru(phen)2dppz2+ (dppz = dipyridophenazine) was employed as the photosensitive intercalator, and ferricytochrome c (Fe3+ cyt c), as the oxidative quencher. Using transient absorption and time-resolved luminescence spectroscopies, we examined the electron-transfer reactions following photoexcitation of the ruthenium complex in the presence of poly(dA-dT) or poly(dG-dC). The luminescence-quenching titrations of excited Ru(phen)2dppz2+ by Fe3+ cyt c are nearly identical for the two DNA polymers. However, the spectral characteristics of the long-lived transient produced by the quenching depend strongly upon the DNA. For poly(dA-dT), the transient has a spectrum consistent with formation of a [Ru(phen)2dppz3+, Fe2+ cyt c] intermediate, indicating that the system regenerates itself via electron transfer from the protein to the Ru(III) metallointercalator for this polymer. For poly(dG-dC), however, the transient has the characteristics expected for an intermediate of Fe2+ cyt c and the neutral guanine radical. The characteristics of the transient formed with the GC polymer are consistent with rapid oxidation of guanine by the Ru(III) complex, followed by slow electron transfer from Fe2+ cyt c to the guanine radical. These experiments show that electron holes on DNA can be repaired by protein and demonstrate how the flash-quench technique can be used generally in studying electron transfer from proteins to guanine radicals in duplex DNA.     

Microglia, major player in the brain inflammation: their roles in the pathogenesis of Parkinson's disease

Inflammation, a self-defensive reaction against various pathogenic stimuli, may become harmful self-damaging process. Increasing evidence has linked chronic inflammation to a number of neurodegenerative disorders including Alzheimer's disease (AD), Parkinson's disease (PD), and multiple sclerosis. In the central nervous system, microglia, the resident innate immune cells play major role in the inflammatory process. Although they form the first line of defense for the neural parenchyma, uncontrolled activation of microglia may directly toxic to neurons by releasing various substances such as inflammatory cytokines (IL-1beta, TNF-alpha, IL-6), NO, PGE(2), and superoxide. Moreover, our recent study demonstrated that activated microglia phagocytose not only damaged cell debris but also neighboring intact cells. It further supports their active participation in self-perpetuating neuronal damaging cycles. In the following review, we discuss microglial responses to damaging neurons, known activators released from injured neurons and how microglia cause neuronal degeneration. In the last part, microglial activation and their role in PD are discussed in depth.     

Transetherification polycondensation: The roles of the catalyst,monomer structure,and polymerization conditions

A detailed study of the novel melt transetherification polycondensation process, which was recently developed in our laboratory, is presented. The efficacy of different catalysts, such as p‐toluenesulfonic acid (PTSA), camphorsulfonic acid, and their pyridinium salts, was examined. The pyridinium salts, especially pyridinium camphorsulfonate (PCS), outperformed PTSA both in terms of the polymer molecular weights (the polydispersity) and the extent of discoloration of the polymer. The evolution of the molecular weight with the polymerization time was monitored with two different catalysts, PTSA and PCS, and these studies demonstrated that, while PTSA yielded polymers with a broad molecular weight distribution, the use of PCS curtailed possible side reactions that led to this broadening. Model reactions suggested that one possible reason for this broadening could be the formation of macrocyclics facilitated by an ether–ether exchange reaction, which was shown to occur much more rapidly when PTSA was used. A further interesting and rather unprecedented feature, which became apparent while the effect of the acid–catalyst concentration was being examined, was the dual role played by the acid, which acted both beneficially as a catalyst and detrimentally, defunctionalizing the chain end and terminating polymer growth. This conclusion was based on the observed decrease in the molecular weight of the polymer at very high catalyst concentrations, which suggested that there existed an optimum catalyst concentration at which a balance was struck between the molecular weight of the polymer formed and the polymerization time. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 102–111, 2004     

Regioisomerism in the synthesis of a chiral aminotetralin drug compound: unraveling mechanistic details and diastereomer-specific in-depth NMR investigations

During chemical process development of a novel 2-aminotetralin derivative intended for use as an antidepressant, scrutiny of the byproduct present in the drug molecule revealed a set of regioisomers. Detailed studies showed that this impurity issue originated from an early synthetic step in which a brominated tetralone motif was generated in a ring-closing protocol. It was found that this reaction was accompanied by a migration of the aromatic bromo substituent via different bromonium species along two discrete pathways. This example of the halogen dance reaction resulted in the formation of a series of tetralone impurities with a bromine distributed across all available aromatic positions of the tetralin nucleus. Subsequently, when subjected to reductive amination conditions, each of these tetralones gave rise to pairs of aminotetralins in a diastereomeric relationship. NMR investigations revealed that the alicyclic portion of the compounds thus formed displayed very complex signal patterns, which required further in-depth studies using a variety of sophisticated techniques. As a result, a deep insight into the structural features of the current 2-aminotetralin family was obtained, which is emphasized by the definition of a novel "0.2 ppm rule" allowing the absolute configuration at tetralin C-2 to be determined.     

A near-infrared Fourier transform Raman spectroscopy of epidermal keratinocytes: changes in the protein-DNA structure following malignant transformation

We report here the use of near-infrared (NIR) Fourier transform (FT) Raman spectroscopy to analyze normal human epidermal keratinocytes prior to and following malignant transformation. Our analysis indicates specific Raman spectral differences between immortalized (HPK1A) and malignant ras transformed (HPK1A-ras) cells. In addition, striking spectral differences are seen in the DNA isolated from these cells and particularly in the 843/810 cm(-1) ratio with values of 1.6 +/- 0.13 in HPK1A cells and 0.68 +/- 0.09 in HPK1A-ras cells (mean +/- S.D., n = 12, P < 0.001) indicating specific alterations in the backbone conformation markers following malignant transformation. Subsequently, we analysed the effect of a strong inhibitor of keratinocyte growth, the Vitamin D analog EB1089, on the Raman spectra of intact cells and on the 843/810 cm(-1) ratio in the DNA isolated from both cell lines. Specific changes were observed in intact cells in the 1300-750 cm(-1) region. Furthermore, the 843/810 cm(-1) ratio of isolated DNA from HPK1A cells was not affected by EB1089 but significantly increased in DNA isolated from HPK1A-ras cells so much that it became closer to the value observed for HPK1A cells (1.07 +/- 0.10). Our data suggest that Raman analysis of DNA and in particular the 843/810 cm(-1) ratio can provide useful indices of malignant transformation and efficacy of anticancer agents.     

Technical solutions for analysis of grape juice,must, and wine: the role of infrared spectroscopy and chemometrics

Information about constituents of grape juice, must, and wine can be used for management and decision support systems in order to improve, monitor, and adapt grape and wine production to new challenges. Numerous sensors that gather this information are either currently available or in development. Nevertheless there is still a need to adapt these sensors to special requirements, for example robustness, calibration and maintenance, operating costs, duration, sensitivity, and specificity to a particular application. The sensors commonly used by the wine industry are those that are based on mid-infrared (MIR), near-infrared (NIR), visible (VIS) and ultraviolet (UV) spectroscopy. This article reviews some recent technical solutions for analysis of juice, must and wine based on the combination of infrared spectroscopy and chemometrics.