Methods for extracting biochemical information from bacterial Raman spectra: focus on a group of structurally similar biomolecules--fatty acids

In this paper we explore the possibilities of Raman spectroscopy in order to deduce information on the fatty acid composition of bacterial cells. Therefore, representative strains of two bacterial taxa were each cultured in different conditions and in parallel analyzed by Raman spectroscopy and gaschromatographic FAME analysis. Raman spectra of pure fatty acids were recorded and used as reference spectra. The culturing conditions for each strain could be easily distinguished by the fatty acid information retrieved from bacterial Raman spectra. Chemometric techniques such as EMSC and PCA allowed to extract information about groups of fatty acids, that was consistent with the results from FAME analysis. Although the information retrieved from Raman spectroscopy is not as refined as that from FAME analysis, the presented methods could be useful to obtain basic information on the fatty acid present in bacteria when performing Raman spectroscopic analysis for fast whole cell profiling, which provides information for different types of cell components (fatty acids, amino acids, primary metabolites, etc.).     

Long-range order in a polycrystalline Pd-30 at % Au solid solution

Using x-ray analysis, at % the existence of regions with a long-range order of the Cu₃Au type has been established in a polycrystalline Pd-30 at % Au solid solution.     

The Co‐Entrapment of a Homogeneous Catalyst and an Ionic Liquid by a Sol–gel Method: Recyclable Ionogel Hydrogenation Catalysts

Molecular hydrogenation catalysts have been co‐entrapped with the ionic liquid [Bmim]NTf₂ inside a silica matrix by a sol–gel method. These catalytic ionogels have been compared to simple catalyst‐doped glasses, the parent homogeneous catalysts, commercial heterogeneous catalysts, and Rh‐doped mesoporous silica. The most active ionogel has been characterised by transmission electron microscopy, X‐ray photoelectron spectroscopy, and solid state NMR before and after catalysis. The ionogel catalysts were found to be remarkably active, recyclable and resistant to chemical change.     

Improved tandem mass spectrometric characterization of 3-nitrotyrosine sites in peptides

Nitrated tyrosines are easily converted into their aminotyrosine equivalents by a reduction step. We here show that this conversion can be exploited to readily discern 3-aminotyrosine peptides in a background of non-nitrated peptides. Furthermore, aminotyrosine peptides are more stable in single mass spectrometry (MS) mode rendering peptide mass maps easier to interpret. One significant caveat of both 3-nitrotyrosine and 3-aminotyrosine peptides is their lack of efficient fragmentation upon collision-induced dissociation (CID) which, in the case of the latter peptides, also produces unexpected, deviating isotopic patterns of fragment ions containing the aminotyrosine residue. The net result is that sequence database searching becomes daunting as the correct peptide is frequently missed since insufficient and/or inaccurate peptide fragments are used. We show that a simple acetylation step, blocking all amines (including aminotyrosine), produces peptides that undergo extensive backbone fragmentation by CID and are thus easily identifiable in databases. Our procedure is additionally illustrated by doubling the number of nitration events mapped in tetranitromethane-nitrated bovine serum albumin (BSA) as compared to a direct analysis of the nitrated peptides using the same amount of material. In conclusion, we here illustrate that this two-step process, heme-mediated reduction and acetylation, can be used for more efficient characterization of protein-bound nitrated tyrosines.     

Multiplexed protein detection using an affinity aptamer amplification assay

Affinity probe capillary electrophoresis (APCE) is potentially one of the most versatile technologies for protein diagnostics, offering an excellent balance between robustness, analysis speed and sensitivity. Combining the immunosensing and separating strength of capillary electrophoresis with the signal enhancement power of nucleic acid amplification, aptamers can further push the analytical limits of APCE to offer ultrasensitive, multiplexed detection of protein biomarkers, even when differences in electrophoretic mobility between the different aptamer-target complexes are limited. It is demonstrated how, through careful selection of experimental parameters, simultaneous detection of picomolar levels of three target proteins can be achieved even with aptamers that were initially selected under very different conditions and further taking into account that the aptamers need to be modified to allow successful PCR amplification. Aptamer-enhanced APCE offers limits of detection that are orders of magnitude lower than those that can be achieved through traditional capillary electrophoresis-based immunosensing. With recent developments in aptamer selection that for the first time realise the promise of aptamers as easily accessible, high affinity recognition molecules, it can therefore be envisioned that aptamer-enhanced APCE on parallel microfluidic platforms can be the basis for a truly high-throughput multiplexed proteomics platform, rivalling genetic screening for the first time.     

Ageing of enteric neurons: oxidative stress, neurotrophic factors and antioxidant enzymes

Background

??Dragon??s Blood?? (DB) has long been used as an ethnomedicine in China to invigorate blood circulation for the treatment of traumatic injuries, blood stasis and pain. To comprehensively assess the quality of DB medicine, a precise and accurate method that can rapidly separate, characterize and quantify multiple active components of DB is crucial.

Results

An ultra performance liquid chromatography (UPLC) coupled with photodiode array detection (PAD) and electrospray ionization mass spectrometry (ESI-MS) method was developed for characterization and determination of six flavonoids in DB. A comprehensive validation of the developed method was conducted, and confirmed that the method presented good sensitivity, precision and accuracy. All linear regressions were acquired with R ² > 0.99, and the limits of detection ranged from 0.06 to 0.83 ng. The relative standard deviation (RSD) values were found to be within the range 1.4?C3.8% for the method repeatability test. Recovery studies for the quantified compounds were found to be within the range 94.2?C102.8% with RSD less than 4.9%. DB samples collected from different geographical regions were analyzed by the present method, and the results demonstrated that the contents of the six flavonoids in DB samples varied significantly. Three major active components among the six flavonoids, namely dracorhodin, (2S)-5-methoxyflavan-7-ol and (2S)-5-methoxy-6-methylflavan-7-ol, are suggested as the index for DB quality evaluation.

Conclusions

Overall, the present hyphenation method is highly efficient and reliable, and hence suitable for the characterization and determination of the flavonoids of DB ethnomedicine.     

Single-cell recording and stimulation with a 16k micro-nail electrode array integrated on a 0.18 μm CMOS chip

To cope with the growing needs in research towards the understanding of cellular function and network dynamics, advanced micro-electrode arrays (MEAs) based on integrated complementary metal oxide semiconductor (CMOS) circuits have been increasingly reported. Although such arrays contain a large number of sensors for recording and/or stimulation, the size of the electrodes on these chips are often larger than a typical mammalian cell. Therefore, true single-cell recording and stimulation remains challenging. Single-cell resolution can be obtained by decreasing the size of the electrodes, which inherently increases the characteristic impedance and noise. Here, we present an array of 16,384 active sensors monolithically integrated on chip, realized in 0.18 μm CMOS technology for recording and stimulation of individual cells. Successful recording of electrical activity of cardiac cells with the chip, validated with intracellular whole-cell patch clamp recordings are presented, illustrating single-cell readout capability. Further, by applying a single-electrode stimulation protocol, we could pace individual cardiac cells, demonstrating single-cell addressability. This novel electrode array could help pave the way towards solving complex interactions of mammalian cellular networks.     

Two Efficient and Practical Syntheses of Methyl 4-Mercaptobenzoate

Two efficient syntheses of methyl 4-mercaptobenzoate are described, one utilizing the dianion of 4-bromothiophenol, the other a S_NAr reaction starting with 4-fluorobenzonitrile.     

Generation of singlet oxygen with the use of optically excited fullerenes and fullerene-like nanoparticles

Experimental results and a kinetic model of generation of singlet oxygen during the interaction of oxygen molecules with optically pumped (lamp or laser radiation) fullerenes or fullerene-like nanoclusters in solutions, suspensions, and the form of various solid-phase membranes (surfaces) are presented. The experimental data on the photoluminescence of singlet oxygen in solutions of fullerenes are compared with the results of numerical simulation on the basis of the kinetic model with specified constants of photochemical processes. On the basis of the experimental results, it is shown that evaporation of a solution caused by pumping radiation yields long-lived gas-phase singlet oxygen. Release of gas-phase singlet oxygen from solid-phase fullerene-containing membranes (surfaces) is also demonstrated; however, this process is hindered by adsorption of singlet oxygen on the membrane surface. The prospects for creation of a singlet-oxygen generator on the basis of photoexcited fullerene molecules and fullerene-like nanoclusters are discussed.     

The structure and EPR properties of (CH2OHCH2NH3)2CuCl4

The title compound is a member of the (RNH₃)₂CuCl₄ layer perovskite family, space group C2/c, witha=21.624(5),b=7.511(1),c=7.431(2)Å, =89.56(2)° andV=1206.9(4)ų withZ=4. In the antiferrodistortive structure, the Cu(II) ion assumes an elongated octahedral coordination (unique Cu–Cl distances=2.274(2), 2.288(2), and 3.010(2)Å). The octahedra share corners with four neighbors to form a two-dimensional network. The –NH₃ moieties hydrogen bond to the layers, so that the –C₂H₅OH moieties form sheathes about each metal halide layer. A twofold disorder of the –C₂H₅OH groups is observed. The EPR spectrum is investigated to help understand the magnetic properties of the systems. Theg-values are consistent with strong intralayer exchange coupling. The EPR linewidths show evidence of spin diffusion effects at liquid nitrogen temperature. However, at room temperature, the spin anisotropies lead to broadening of the EPR lines through a phonon modulation mechanism.