Gene polymorphism of interleukin 1 and 8 in chronic gastritis patients infected with Helicobacter pylori

Background: Epidemiological investigations have indicated that Helicobacter pylori induces inflammation in the gastric mucosa regulated by several interleukins. the genes IL1B and IL8 are suggested as key factors in determining the risk of gastritis. the aim of this paper was to evaluate the association of gene polymorphism of interleukin-1 and interleukin-8 with chronic gastrits in H. pylori infected patients. A total of 60 patients underwent endoscopic procedure. Biopsy samples were collected for urease test, histopathological and molecular exams. the DNA of theses samples was extracted for detection of H. pylori and analysis of the genes mentioned above. Patients with gastritis had a higher frequency of H. pylori-positive samples.Results: H. pylori was detected in 30/60 patients (50%) by PCR. As for polymorphism of interleukin 8 (-251) gene we observed a statistical difference when analyzed TA (p = 0.039) and TT (p = 0.047) genotypes. in the IL1B31 there was a statistical difference in TT (p = 0.01) genotype and in the IL1B-511 there wasn't any statistical difference.Conclusion: Our results suggest a strong correlation between the presence of chronic gastritis and infection by H. pylori and that IL1B-31TT and IL8-251TT genotypes appear to act as protective factors against H. pylori infection while IL8-251TA genotype may comprise a risk factor for infection with this bacterium.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Marilia Medical SchoolMarilia Med Sch FAMEMA, FAMEMA Blood Ctr, Dept Genet, Marilia, SP, BrazilSacred Heart Univ USC, Bauru, SP, BrazilMarilia Med Sch FAMEMA, Dept Digest Syst Surg, Marilia, SP, BrazilFed Univ São Paulo UNIFESP, Dept Morphol, São Paulo, BrazilMarilia Med Sch FAMEMA, Dept Radiotherapy & Oncol, Marilia, SP, BrazilFAMEMA, Hemoctr, Genet Lab, BR-17519050 São Paulo, BrazilFed Univ São Paulo UNIFESP, Dept Morphol, São Paulo, BrazilFAPESP: 0915857-9Web of Scienc

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Radiation damage by extensive local water ionization from two-step electron-transfer-mediated decay of solvated ions

Biomolecular radiation damage is largely mediated by radicals and low-energy electrons formed by water ionization rather than by direct ionization of biomolecules. It was speculated that such an extensive, localized water ionization can be caused by ultrafast processes following excitation by core-level ionization of hydrated metal ions. In this model, ions relax via a cascade of local Auger–Meitner and, importantly, non-local charge- and energy-transfer processes involving the water environment. Here, we experimentally and theoretically show that, for solvated paradigmatic intermediate-mass Al3+ ions, electronic relaxation involves two sequential solute–solvent electron transfer-mediated decay processes. The electron transfer-mediated decay steps correspond to sequential relaxation from Al5+ to Al3+ accompanied by formation of four ionized water molecules and two low-energy electrons. Such charge multiplication and the generated highly reactive species are expected to initiate cascades of radical reactions

Attosecond formation of charge-transfer-to-solvent states of aqueous ions probed using the core-hole-clock technique

Charge transfer between molecules lies at the heart of many chemical processes. Here, we focus on the ultrafast electron dynamics associated with the formation of charge-transfer-to-solvent (CTTS) states following X-ray absorption in aqueous solutions of Na+, Mg2+, and Al3+ ions. To explore the formation of such states in the aqueous phase, liquid-jet photoemission spectroscopy is employed. Using the core-hole-clock method, based on Auger–Meitner (AM) decay upon 1s excitation or ionization of the respective ions, upper limits are estimated for the metal-atom electron delocalization times to the neighboring water molecules. These delocalization processes represent the first steps in the formation of hydrated electrons, which are determined to take place on a timescale ranging from several hundred attoseconds (as) below the 1s ionization threshold to only 20 as far above the 1s ionization threshold. The decrease in the delocalization times as a function of the photon energy is continuous. This indicates that the excited electrons remain in the vicinity of the studied ions even above the ionization threshold, i.e., metal-ion electronic resonances associated with the CTTS state manifolds are formed. The three studied isoelectronic ions exhibit quantitative differences in their electron energetics and delocalization times, which are linked to the character of the respective excited states

Probing aqueous ions with non-local Auger relaxation

Non-local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non-local autoionization, specifically Intermolecular Coulombic Decay (ICD), of a series of aqueous-phase isoelectronic cations following 1s core-level ionization. In particular, we focus on Na+, Mg2+, and Al3+ ions. We unambiguously identify the ICD contribution to the K-edge Auger spectrum. The different strength of the ion-water interactions is manifested by varying intensities of the respective signals: the ICD signal intensity is greatest for the Al3+ case, weaker for Mg2+, and absent for weakly-solvent-bound Na+. With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non-local decay processes. We assign the ICD signals to decay processes ending in two-hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core-hole-clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2+ and 34 fs for Al3+. Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra- and inter-molecular structure in the liquid phase, simultaneously providing both structural and electronic information

Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse

Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed

Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography

Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 angstrom resolution and determine its serial femtosecond crystallography structure to 3.5 angstrom resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure

X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e.g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules

Sub-nanometer-scale measurements of the interaction of ultrafast soft x-ray free-electron-laser pulses with matter

Femtosecond pulses from soft-x-ray free-electron lasers (FELs) [1] are ideal for directly probing matter at atomic length scales and timescales of atomic motion. An important component of understanding ultrafast phenomena of light-matter interactions is concerned with the onset of atomic motion which is impeded by the atoms inertia. This delay of structural changes will enable atomic-resolution flash-imaging [2-3] to be performed at upcoming x-ray FELs [4-5] with pulses intense enough to record the x-ray scattering from single molecules [6]. We explored this ultrafast high-intensity regime with the FLASH soft-x-ray FEL [7-8] by measuring the reflectance of nanostructured multilayer mirrors using pulses with fluences far in excess of the mirrors damage threshold. Even though the nanostructures were ultimately completely destroyed, we found that they maintained their integrity and reflectance characteristics during the 25-fs-long pulse, with no evidence for any structural changes during that time over lengths greater than 3 {angstrom}. In the recently built FLASH FEL [7], x-rays are produced from short electron pulses oscillating in a periodic magnet array, called an undulator, by the principle of self-amplification of spontaneous emission [9-10]. The laser quality of the x-ray pulses can be quantified by the peak spectral brilliance of the source, which is 10{sup 28} photons/(s mm2 mrad2 0.1% bandwidth) [8]; this is up to seven orders of magnitude higher than modern third-generation synchrotron sources. For our studies, the machine operated with pulses of 25 fs duration at a wavelength of 32.5 nm and energies up to 21 {micro}J. We focused these pulses to 3 x 10{sup 14} W/cm{sup 2} onto our nanostructured samples, resulting in an the unprecedented heating rate of 5 x 10{sup 18} K/s, while probing the irradiated structures at the nanometer length scale. The x-ray reflectivity of periodic nanometer-scale multilayers [11] is very sensitive to changes in the atomic positions and the refractive indices of the constituent materials, making them an ideal choice to study structural changes induced by ultrashort FEL pulses. The large multilayer reflectivity results from the cooperative interaction of the x-ray field with many layers of precisely fabricated thicknesses, each less than the x-ray wavelength. This Bragg or resonant reflection from the periodic structure is easily disrupted by any imperfection of the layers. The characteristics of the structure, such as periodicity or layer intermixing, can be precisely determined from the measurement of the Bragg reflectivity as a function of incidence angle. These parameters can be easily measured to a small fraction of the probe wavelength, as is well known in x-ray crystallography where average atomic positions of minerals or proteins are found to less than 0.01{angstrom}. Thus, we can explore ultrafast phenomena at length scales less than the wavelength, and investigate the conditions to overcome the effects of radiation damage by using ultrafast pulses