Fragmentation trees for the structural characterisation of metabolites

Metabolite identification plays a crucial role in the interpretation of metabolomics research results. Due to its sensitivity and widespread implementation, a favourite analytical method used in metabolomics is electrospray mass spectrometry. In this paper, we demonstrate our results in attempting to incorporate the potentials of multistage mass spectrometry into the metabolite identification routine. New software tools were developed and implemented which facilitate the analysis of multistage mass spectra and allow for efficient removal of spectral artefacts. The pre-processed fragmentation patterns are saved as fragmentation trees. Fragmentation trees are characteristic of molecular structure. We demonstrate the reproducibility and robustness of the acquisition of such trees on a model compound. The specificity of fragmentation trees allows for distinguishing structural isomers, as shown on a pair of isomeric prostaglandins. This approach to the analysis of the multistage mass spectral characterisation of compounds is an important step towards formulating a generic metabolite identification method. Copyright ? 2012 John Wiley & Sons, Ltd.     

A theoretical study of hemiacetal formation from the reaction of methanol with derivatives of CX3CHO (X = H,F, Cl,Br and I)

A theoretical study of the hemiacetal formation reaction between methanol and CX₃CHO (X = H, F, Cl, Br, and I) has been carried out using density functional theory and Becke, three‐parameter, Lee–Yang–Parr/6‐311++G(d,p) computational methods. The stationary points of the reaction between the isolated molecules and the reaction catalyzed by an additional methanol molecule have been characterized. Because the final products present a stereogenic center, the potential autocatalysis of the reaction has been examined and also the possibility of spontaneous generation of chirality when the hemiacetal molecules are involved in the transition state structure. High barriers are found in the reaction between the isolated molecules that are reduced by the assistance of an additional molecule (methanol or hemiacetal product). The reactions catalyzed by the hemiacetal products show higher barriers than the one catalyzed by methanol. Copyright © 2012 John Wiley & Sons, Ltd.     

Physical methods for genetic plant transformation

Production of transgenic plants is a routine process for many crop species. Transgenes are introduced into plants to confer novel traits such as improved nutritional qualities, tolerance to pollutants, resistance to pathogens and for studies of plant metabolism. Nowadays, it is possible to insert genes from plants evolutionary distant from the host plant, as well as from fungi, viruses, bacteria and even animals. Genetic transformation requires penetration of the transgene through the plant cell wall, facilitated by biological or physical methods. The objective of this article is to review the state of the art of the physical methods used for genetic plant transformation and to describe the basic physics behind them.     

Morphology and thermal stability of AlF3 thin films grown on Cu(100)

The growth of ultrathin epitaxial layers of aluminum fluoride on Cu(100) has been studied by a combination of surface science techniques. Deposition at room temperature results in step decoration followed by the formation of dendritic two-dimensional islands that coalesce to form porous films. Ultrathin layers (up to 2 monolayers in thickness) are morphologically unstable upon annealing; de-wetting takes place around 430 K with the formation of three-dimensional islands and leaving a large fraction of the Cu surface uncovered. Films several nanometers thick, on the contrary, are stable up to ca. 730 K where desorption in molecular form sets on. The effect of electron irradiation on the AlF₃ has also been characterized by different spectroscopic techniques; we find that even small quantities of stray electrons from rear electron beam heating can provoke significant decomposition of the aluminum fluoride, resulting in the release of molecular fluorine and the formation of deposits of metallic aluminum. These features make AlF₃ an interesting material for spintronic applications.     

Silicon nanowire and polyethylene superhydrophobic surfaces for discrete magnetic microfluidics

A microfluidic method to manipulate small drops of water is studied on two different superhydrophobic surfaces. Using this digital magnetofluidic method, water drops containing paramagnetic carbonyl-iron microparticles were displaced on silicon nanowire (Si NW) and low-density polyethylene (LDPE) superhydrophobic surfaces using magnetic fields. Horizontal, vertical, or upside-down drop movement is made possible by the action of capillary forces induced by paramagnetic particles aligning and following a magnetic field, indicating that three-dimensional digital microfluidics is possible. Also, both Si NW and LDPE superhydrophobic surfaces combine surface chemistry with nano and microscale surface roughness to make drop movement possible. Si NW superhydrophobic surfaces were prepared using vapor-liquid-solid growth systems followed by coating with a perfluorinated hydrocarbon. LDPE superhydrophobic surfaces were prepared by growing polyethylene crystals on a polyethylene substrate through careful rate control.     

Gouy wave modes: undistorted pulse focalization in a dispersive medium

Gouy wave modes are linear waves with finite energy that propagate without distortion at any phase and group velocity through a focal region in a dispersive medium. These features make them potentially useful for the onset and control of nonlinear interactions.     

Iron homeostasis in neuronal cells: a role for IREG1

Background  

Iron is necessary for neuronal function but in excess generates neurodegeneration. Although most of the components of the iron homeostasis machinery have been described in neurons, little is known about the particulars of their iron homeostasis. In this work we characterized the response of SH-SY5Y neuroblastoma cells and hippocampal neurons to a model of progressive iron accumulation.     

Vibrational Spectrometry Strategies for Quality Control of Procymidone in Pesticide Formulations

Abstract

Two vibrational spectrometry–based methodologies were developed for procymidone determination in wettable powdered pesticide formulations. The Fourier‐transform infrared (FTIR) procedure was based on the selective extraction of procymidone by chloroform and determination by peak area measurement between 1451 and 1441 cm^?1, using a baseline correction established between 1490 and 1410 cm^?1, and a precision of 0.4% and a limit of detection of 0.01% w/w procymidone for a sample mass of 25 mg were obtained. For FT‐Raman determination, the selected conditions were peak area measurement between 1005 and 995 cm^?1 Raman shift, with a baseline correction fixed between 1030 and 947 cm^?1, and a relative standard deviation of 1% and a limit of detection of 0.8% procymidone in the original sample were obtained. The sample frequency for FTIR determination was 30 hr^?1, lower than that for Raman with 40 hr^?1. FT‐Raman reduces to the minimum the reagent consumption and waste generation, also avoiding the sample handling and contact of the operator with the pesticide. It can be concluded that the proposed methods are appropriate for quality control in commercial pesticide formulations.     

Modelling non-equilibrium self-assembly from dissipation

Non-equilibrium self-assembly is ubiquitous in physico-chemical and biological systems, and manifests itself at different scales, ranging from the molecular to the cosmological. The formation of microtubules, gels, cells and living beings among many others takes place through self-assembly under nonequilibrium conditions. We propose a general thermodynamic non-equilibrium model to understand the formation of assembled structures such as gels and Liesegang patterns and at the same time able to describe the kinetics and the energetics of the structure formation process. The model is supported for a global mechanism to obtain self-assembled structures from building blocks via activation, deactivation, assembly, and disassembly processes. It is proposed that the resulting structures can be characterised by a structural parameter. Our model may contribute to a better understanding of non-equilibrium self-assembly processes and give deeper insight as to how to obtain a specific structural architecture to materials, such as hydrogels which are of great importance in the design of advanced devices and novel materials.