Analysis Of Molecular Composition Research Articles

Selective Methylation of Sulfides in Petroleum for Electrospray Ionization Mass Spectrometry Analysis

A method for selective methylation of sulfides (particularly aliphatic sulfides) but not thiophenes in petroleum has been developed for positive-ion electrospray ionization (ESI) mass spectrometry. The new method uses only CH3I without AgBF4 to produce methyl sulfonium ions of sulfides for molecular composition analysis. It provides simplicity and saves time compared to a previously developed methylation method using CH3I/AgBF4 to methylate all sulfur compounds into ionic species analyzable by positive-ion ESI. The composition of sulfides by this method agrees with that of the sulfide fraction obtained from CH3I/AgBF4 methylation/demethylation. Hence, the separation of sulfides from thiophenes through elaborate procedures is eliminated. The new method was validated by model compounds and has been successfully applied to the analysis of sulfides in diesel, vacuum gas oil, crude oil, and atmospheric pressure distillation residue. When combined with the previously developed CH3I/AgBF4 method, the new method may have the potential to differentiate reactive sulfur, such as sulfides, from nonreactive sulfur, such as thiophenes. This could provide a means to develop correlations between sulfur types and corrosion, and possibly for other studies.

Actin Microridges.

Microridges are highly distinctive "fingerprint"-patterned structures situated on the outer surface of superficial layer cells of the epithelium. An F-actin-based cytoskeleton is the underlying core structural component of microridges. The basis for much of what is known about microridges has been provided by in vivo and in vitro fish epithelial systems. Nonetheless the microridge literature is quite small, especially when compared with other actin-based cellular structures such as those involved in cell motility. A PubMed search of the terms "Microridges" yields 261 citations from the mid-1970s to the writing of this review. "Microplicae," an alternative name for microridges, and "Actin Microridges" search terms give 204 and 8 references, respectively, in the same time period. By comparison a search of "Lamellipodia" over the same time period yields over 6,400 citations for this important motility structure while a search of the associated "filopodia" results in close to 7,300 articles. Despite the near-ubiquity of microridges in epithelia across species the study of these structures has clearly been neglected. In-depth analysis of microridge molecular composition is very limited while their function remains unclear. This review draws upon information derived from studies of fish as well as mammalian species to provide a more comprehensive view of these structures. The wide-spread distribution of these structures between species and various tissues indicate the microridges have important and common functions in healthy organisms. Conversely, disease conditions may show alterations in microridge structure and function and thus warrant further investigation. Anat Rec, 301:2037-2050, 2018. © 2018 Wiley Periodicals, Inc.

Removal of bioavailable dissolved organic nitrogen in wastewater by membrane bioreactors as posttreatment: Implications for eutrophication control

Bioavailable dissolved organic nitrogen (ABDON) is the component of dissolved organic nitrogen (DON) which supports the growth of algae. Previous research indicates that a membrane bioreactor (MBR) is effective in reducing DON, however, its ability to remove ABDON remains unknown. The present study investigated three full-scale MBRs (membrane type: hydrophilic polyvinylidene fluoride and membrane pore size: 0.04–0.1 µm) as posttreatment for the removal of ABDON. Results showed that the concentrations of ABDON were not significantly different between influent and effluent at each MBR (p = 0.067–0.614, t-test). Analysis of DON molecular composition via ultrahigh resolution mass spectrometry provides supporting evidence that bacterial biomass produced/released ABDON during the biological processes, which would be one of the possible reasons for the low removal efficiency of ABDON (<0%−14.0%) occurred in the MBR process. Overall, MBRs as posttreatments would have a smaller-than expected impact on primary productivity in receiving waters since a substantial fraction of DON stimulating algal growth cannot be removed by this treatment.

Exosomes as emerging players in cancer biology

Oncologic diseases do not behave as isolated entities. Instead, they are based on complex systemic networks involving cell-cell communication between cancerous and healthy cells of the host, which may either facilitate or prevent cancer progression. In addition to cell-cell contacts, cells communicate through secreted factors in a process modulated by ligand concentration, receptor availability and synergy amongst several signaling circuits. Of these secreted factors, exosomes, 30–150 nm membrane vesicles of endocytic origin released by virtually all cells, have emerged as important cell-cell communication players both in physiological and pathological scenarios by being carriers of all the main biomolecules, including lipids, proteins, DNAs, messenger RNAs and microRNA, and performing intercellular transfer of components, locally and systemically. By acting both in tumor and non-tumor cells, such as fibroblasts, leukocytes, endothelial and progenitor cells, tumor- and non-tumor cells-derived exosomes can modulate tumor growth and invasion, tumor-associated angiogenesis, tissue inflammation and the immune system. In this Review, we summarize the main findings of the literature on the roles of exosomes in mediating interactions between tumor and tumor-associated cells. We also discuss how the molecular composition analysis of circulating exosomes in clinical settings has emerged as an attractive non-invasive source of liquid biopsies for early diagnosis, prognosis and follow-up of patients with oncologic diseases.

Blue Native PAGE: Applications to Study Peroxisome Biogenesis.

Blue native polyacrylamide gel electrophoresis (BN-PAGE) is one of the useful methods to isolate protein complexes including membrane proteins under native conditions. In BN-PAGE, Coomassie Brilliant Blue G-250 binds to proteins and provides a negative charge for the electrophoretic separation without denaturing at neutral pH, allowing the analysis of molecular mass, oligomeric state, and composition of native protein complexes. BN-PAGE is widely applied to the characterization of soluble protein complexes as well as isolation of membrane protein complexes from biological membranes such as the complexes I-V of the mitochondrial respiratory chain and subcomplexes of the mitochondrial protein import machinery. BN-PAGE has also been introduced in the field of peroxisome research, for example, analysis of translocation machinery for peroxisomal matrix proteins embedded in the peroxisomal membrane. Here, we describe a basic protocol of BN-PAGE and its application to the study of peroxisome biogenesis.

The simulation of UV spectroscopy and electronic analysis of temozolomide and dacarbazine chemical decomposition to their metabolites

The electronic features of anti-tumor agent, temozolomide, and its degradation products (MTIC and metabolite AIC) have been traced by means of UV absorption spectroscopy in vacuo and aqueous media. For comparison, electronic spectra of related structures and drugs (e.g., dacarbazine) were also investigated. These investigations were carried out using time-dependent density functional theory (TD-DFT) method while the conductor like screening model (COSMO) were applied for the inclusion of solvent effects in electronic spectra. From functional benchmarking, two methods; B3LYP and O3LYP were selected among several other methods with 6-311+G(2d,p) basis set aiming to get the best results in accord with the experimental values. An assessment of the obtained spectra has shown that O3LYP functional gives a mean absolute error (MAE) from experimental absorption peaks of 4.3nm compared to the 7.2nm MAE value at B3LYP level in aqueous media. Furthermore, since the structural and tautomeric conformers affect the electronic spectra, conformational preferences have been analyzed in temozolomide, dacarbazine, and their related structures. Temozolomide structure possesses two rotamers that differ in the orientation of carboxamide moiety with a small energy difference (energy difference of 1.39kcal mol-1 in vacuo and 0.35kcal mol-1 in aqueous media at B3LYP/6-311++G(2df,3pd). The more stable and meta-stable TMZ rotamer have shown their absorption maxima at 329-334nm, respectively, at O3LYP level in aqueous media. Applying statistical calculation according to Boltzmann population formula at 25°C and computed weighed mean estimates the λmax of temozolomide at 331nm, which is in notable agreement with the experimental value (330nm). Moreover, molecular orbital composition analysis has been conducted in order to interpret these findings. Graphical Abstract Temozolomide and dacarbazine.

Poly (Ethylene Terephthalate)‐ZnO Nanocomposites: Optical and Raman Studies

SummaryThe present study reveals the optical properties of PET‐ZnO nanocomposites. The ZnO nanoparticles have been prepared by chemical route. The average size of nanoparticles has been found as ∼16 nm by XRD patterns, where particle size has been calculated using Debye‐Scherrer's formula. The band gap and extinction coefficient have been calculated using absorption spectra, recorded using Perkin Elmer Lambda 750 double beam Spectrophotometer. The UV‐Vis results show that band gap decreases with the increase of wt% of nanoparticles in the nanocomposites due to less band gap of ZnO nanoparicles where as extinction coefficient decreases with the increase in wavelength due to increase of charges carries. For the analysis of molecular vibrations and composition of PET and its nanocomposites with ZnO, WITec CRM 2000 Raman spectrometer coupled with a high resolution Confocal optical microscope has been taken.

Transformation of organic matter in the Holocene sediments of Lake Ochki (south Baikal region): Evidence from pyrolysis data

Transformation of organic matter (OM) in Holocene sediments of Lake Ochki (southern coast of Lake Baikal) at the early stages of diagenesis has been studied using pyrolytic methods of Rock Eval (RE-pyrolysis) and pyrolysis-gas chromatography-mass spectrometry (Pyr-GC-MS). OM has been analyzed in lacustrine sediments and their main producers, phytoplankton and zooplankton. Data on the distribution of hydrocarbon–biomarkers in sediments indicate an uninterrupted influx of terrigenous OM and transformation of OM precipitated by microorganisms. The analysis of molecular composition of pyrolysates makes it possible to assume a sharp change of sedimentation conditions in the upper part of sedimentary sequence (0–60 cm). It is shown that the macromolecular aliphatic kerogen structure begins to form in incoherent sediment at the very early stages of diagenesis.

High-resolution NMR spectroscopy in inhomogeneous fields

High-resolution NMR spectroscopy, providing information on chemical shifts, J coupling constants, multiplet patterns, and relative peak areas, is a mainstream tool for analysis of molecular structures, conformations, compositions, and dynamics. Generally, a homogeneous magnetic field is a prerequisite for obtaining high-resolution NMR information. Magnetic field inhomogeneity, whether from non-ideal experimental conditions or from intrinsic magnetic susceptibility discontinuities in samples, represents a hurdle for applications of high-resolution NMR. Numerous techniques have been proposed for measuring high-resolution NMR spectra free from the influence of inhomogeneous magnetic fields. Besides developments and improvements in NMR instrumentation, various types of experimental approaches have been established for recovering NMR information in inhomogeneous magnetic fields. Three main types are systematically described in this review. In addition, other high-resolution NMR approaches or data processing methods are also briefly described. All high-resolution NMR approaches covered in this review have individual advantages and disadvantages in practical applications, and no one technique is applicable to all practical circumstances. Hence, they are complementary for high-resolution NMR applications in inhomogeneous fields. The underlying mechanisms of these approaches are presented, together with analyses of their applicability and efficiency.

Resolving the structure of inner ear ribbon synapses with STED microscopy.

Synapses are diverse in form and function; however, the mechanisms underlying this diversity are poorly understood. To illuminate structure/function relationships, robust analysis of molecular composition and morphology is needed. The molecular-anatomical components of synapses-vesicles, clusters of voltage-gated ion channels in presynaptic densities, arrays of transmitter receptors in postsynaptic densities-are only tens to hundreds of nanometers in size. Measuring the topographies of synaptic proteins requires nanoscale resolution of their molecularly specific labels. Super-resolution light microscopy has emerged to meet this need. Achieving 50 nm resolution in thick tissue, we employed stimulated emission depletion (STED) microscopy to image the functionally and molecularly unique ribbon-type synapses in the inner ear that connect mechano-sensory inner hair cells to cochlear nerve fibers. Synaptic ribbons, bassoon protein, voltage-gated Ca(2+) channels, and glutamate receptors are inhomogeneous in their spatial distributions within synapses; the protein clusters assume variations of shapes typical for each protein specifically at cochlear afferent synapses. Heterogeneity of substructure among these synapses may contribute to functional differences among auditory nerve fibers. The morphology of synaptic voltage-gated Ca(2+) channels matures over development in a way that depends upon bassoon protein, which aggregates in similar form. Functional properties of synaptic transmission appear to depend on voltage-gated Ca(2+) channel cluster morphology and position relative to synaptic vesicles. Super-resolution light microscopy is a group of techniques that complement electron microscopy and conventional light microscopy. Although technical hurdles remain, we are beginning to resolve the details of molecular nanoanatomy that relate mechanistically to synaptic function.

Image analysis of Caenorhabditis elegans ciliary transition zone structure, ultrastructure, molecular composition, and function.

The transition zone (TZ) at the ciliary base has emerged as an important regulator of the composition and functions of cilia, which are microtubule-based structures extending from the surfaces of most eukaryotic cells, serving motility, chemo-/mechano-/photosensation and developmental signaling roles. Possessing distinct ultrastructural features such as microtubule-membrane spanning Y-links, the ∼0.2-1.0-μm long TZ is thought to act as a gated cytosolic (size dependent) and membrane diffusion barrier that drives ciliary compartmentalization by preventing unregulated protein exchange between the cilium and the rest of the cell. Multiple proteins associated with ciliary diseases (ciliopathies) such as Meckel-Gruber syndrome (MKS) and nephronophthisis are specifically found in the TZ, and work from a number of model systems, including Chlamydomonas reinharditii, Caenorhabditis elegans and the mouse indicates TZ-gating and associated ciliogenic functions for a number of these proteins. Here we present a suite of assays for probing the structure, function, and molecular composition of the C. elegans TZ, with emphasis on TZ ultrastructure, diffusion barrier kinetics, MKS module assembly hierarchy, and TZ-dependent behaviors.

Molecular Characterization, Compositional Analysis, and Germination Evaluation of a High‐Oleic Soybean Generated by the Suppression ofFAD2‐1Expression

ABSTRACTSoybean [Glycine max(L.) Merr.] oil is one of the most consumed and highest produced vegetable oils. However, the high percentage of polyunsaturated fatty acids in soybean oil limits its stability and shelf life. Here we report the generation and characterization of a high oleic acid soybean event (305423 soybean) that has an elevated content of monounsaturated oleic acid and reduced presence of polyunsaturated linoleic acid and linolenic acid. This transgenic event was generated by the insertion of a soybean ω‐6 desaturase (FAD2) gene fragment (gm‐fad2‐1), resulting in the suppression of endogenousFAD2‐1expression, and a modified version of the soybeanacetolactate synthase(ALS) gene (gm‐hra), used as a selectable marker. Molecular characterization revealed that 305423 soybean harbors four DNA inserts containing multiple copies of complete and partialgm‐fad2‐1gene cassettes and a single copy of the intactgm‐hragene cassette. However, these DNA inserts seemed to be inherited together without segregation. The suppression of endogenousFAD2‐1led to an increase of oleic acid (18:1) from 211 to 765 g kg–1along with concurrent reduction of both linoleic acid (18:2) from 525 to 36.2 g kg–1and linolenic acid (18:3) from 93.5 to 53.9 g kg–1out of total fatty acyl groups. The 305423 soybean was also subjected to nutrient composition analyses and phenotypic and agronomic performance evaluations and found to be comparable to the control soybean except for the expected traits.

Potential for Aerobic Methane Oxidation in Carboniferous Coal Measures

Carbon (C), geologically sequestered in coal, is gradually released to the atmosphere as CH4 and CO2. Recent anthropogenic activity (coal mining) has rapidly increased the rate of C reallocation from coal deposits into the atmosphere, which has deleterious effect on the climate as both gases are effective infrared absorbers. In the current study we demonstrate that the coal bearing sedimentary rocks possess potential of biological methane oxidation. Viable methanotrophic bacteria, capable of methane oxidation at ambient air and a range of methane concentrations were found in coalbearing formations of the Upper Silesian (USCB) and Lublin Coal Basins (LCB). Factors controlling activity of the aerobic methanotrophic bacteria in the deep subsurface such as, depth, methane concentration, available electron acceptors, moisture and nutrients availability were investigated along with paleoenvironmental factors (temperature changes during and after burial and paleohydrological infiltration). The distribution and activity of the methanotrophic bacteria in the deep subsurface were found to be influenced by geological conditions among which evolution of paleotemperatures and paleohydrological conditions play a predominant role. The data presented along with analysis of molecular composition of the coalbed gases in various coal basins worldwide has led to the conclusion that aerobic methanotrophy may be a widespread process, which, to our knowledge, so far has not been included in investigations concerning C cycling in the subsurface.

The role of lipid metabolism in the acquisition of desiccation tolerance in Craterostigma plantagineum: a comparative approach

Dehydration leads to different physiological and biochemical responses in plants. We analysed the lipid composition and the expression of genes involved in lipid biosynthesis in the desiccation-tolerant plant Craterostigma plantagineum. A comparative approach was carried out with Lindernia brevidens (desiccation tolerant) and two desiccation-sensitive species, Lindernia subracemosa and Arabidopsis thaliana. In C.plantagineum the total lipid content remained constant while the lipid composition underwent major changes during desiccation. The most prominent change was the removal of monogalactosyldiacylglycerol (MGDG) from the thylakoids. Analysis of molecular species composition revealed that around 50% of 36:x (number of carbons in the acyl chains: number of double bonds) MGDG was hydrolysed and diacylglycerol (DAG) used for phospholipid synthesis, while another MGDG fraction was converted into digalactosyldiacylglycerol via the DGD1/DGD2 pathway and subsequently into oligogalactolipids by SFR2. 36:x-DAG was also employed for the synthesis of triacylglycerol. Phosphatidic acid (PA) increased in C.plantagineum, L.brevidens, and L.subracemosa, in agreement with a role of PA as an intermediate of lipid turnover and of phospholipase D in signalling during desiccation. 34:x-DAG, presumably derived from de novo assembly, was converted into phosphatidylinositol (PI) in C.plantagineum and L.brevidens, but not in desiccation-sensitive plants, suggesting that PI is involved in acquisition of desiccation tolerance. The accumulation of oligogalactolipids and PI in the chloroplast and extraplastidial membranes, respectively, increases the concentration of hydroxyl groups and enhances the ratio of bilayer- to non-bilayer-forming lipids, thus contributing to protein and membrane stabilization.

Molecular mobility, composition and structure analysis in glycerol plasticised chitosan films

This study was developed with the purpose to investigate the effect of polysaccharide/plasticiser concentration on the microstructure and molecular dynamics of polymeric film systems, using transmission electron microscope imaging (TEM) and nuclear magnetic resonance (NMR) techniques. Experiments were carried out in chitosan/glycerol films prepared with solutions of different composition. The films obtained after drying and equilibration were characterised in terms of composition, thickness and water activity.Results show that glycerol quantities used in film forming solutions were responsible for films composition; while polymer/total plasticiser ratio in the solution determined the thickness (and thus structure) of the films. These results were confirmed by TEM.NMR allowed understanding the films molecular rearrangement. Two different behaviours for the two components analysed, water and glycerol were observed: the first is predominantly moving free in the matrix, while glycerol is mainly bounded to the chitosan chain.

Experimental Determination of k-Values and Compositional Analysis of Liquid Phases in the Liquid–Liquid Equilibrium Study of (Athabasca Bitumen + Ethane) Systems

Phase behavior properties of (bitumen + solvent) systems have a significant effect on surface upgrading methods and are necessary for the recovery of bitumen from reservoir. In this study, the phase partitioning and component distribution between phases as well as phase properties at equilibrium condition for the (Athabasca bitumen + ethane) system at room temperature were experimentally evaluated. The experiments were conducted using a designed pressure–volume–temperature (PVT) apparatus to obtain liquid–liquid equilibrium properties as well as extraction yield for (bitumen + solvent) systems. In addition, the equilibrium k-value for each component present in the mixture at equilibrium condition was calculated on the basis of compositional analysis of liquid phases and available correlations for the molecular weight of heavy components. The impact of pressure and solvent to bitumen ratio on the boiling point curves and compositional analysis of flashed off liquids as well as equilibrium k-values were evaluated. Finally, the molecular weight of flashed off liquid phase samples were estimated on the basis of molecular weight and compositional analysis of liquids.

Synthesis of biomorphic SiC ceramics from coir fibreboard preform

Coir fibre, an agricultural waste material of immense economic importance in Indian subcontinent, was used as a precursor to biomorphic SiC ceramics. Fibreboards made of coir fibres were converted to carbon templates by controlled thermal processing. Plant material precursors were characterised by analysis of molecular composition, by determination of bulk density and by scanning electron microscopy. Carbon templates were characterised by measurement of dimensional shrinkages, mass loss and bulk density and by scanning electron microscopy and XRD. The carbon templates were further subjected to infiltration with liquid Si at 1550°C under vacuum, when spontaneous infiltration and reaction yielded composite ceramics preserving the morphology of native coir fibre derived precursors on macro and micro scale. The resulting material had a density of 2.59gcm−3 and, on a microstructural scale, contained SiC and Si in addition to carbon (trace) and porosity (2vol%). The end ceramics offered room temperature flexural strength of 116MPa and elastic modulus of 167GPa. Fractographic examination indicated brittle failure. The biomorphic SiC material derived from coir fibreboard precursor is likely to be suitable for use in advanced engineering applications as structural ceramics.

Structure of Alginate Gels: Interaction of Diuronate Units with Divalent Cations from Density Functional Calculations

The complexation of (1→4) linked α-L-guluronate (G) and β-D-mannuronate (M) disaccharides with Mg(2+), Ca(2+), Sr(2+), Mn(2+), Co(2+), Cu(2+), and Zn(2+) cations have been studied with quantum chemical density functional theory (DFT)-based method. A large number of possible cation-diuronate complexes, with one and two GG or MM disaccharide units and with or without water molecules in the inner coordination shells have been considered. The computed bond distances, cation interaction energies, and molecular orbital composition analysis revealed that the complexation of the transition metal (TM) ions to the disaccharides occurs via the formation of strong coordination-covalent bonds. On the contrary, the alkaline earth cations form ionic bonds with the uronates. The unidentate binding is found to be the most favored one in the TM hydrated and water-free complexes. By removing water molecules, the bidentate chelating binding also occurs, although it is found to be energetically less favored by 1 to 1.5 eV than the unidentate one. A good correlation is obtained between the alginate affinity trend toward TM cations and the interaction energies of the TM cations in all studied complexes, which suggests that the alginate affinities are strongly related to the chemical interaction strength of TM cations-uronate complexes. The trend of the interaction energies of the alkaline earth cations in the ionic complexes is opposite to the alginate affinity order. The binding strength is thus not a limiting factor in the alginate gelation in the presence of alkaline earth cations at variance with the TM cations.

Tuning Nonlinear Optical and Optoelectronic Properties of Vinyl Coupled Triazene Chromophores: A Density Functional Theory and Time-Dependent Density Functional Theory Investigation

Triazenes are a unique class of polyazo compounds containing three consecutive nitrogen atoms in an acyclic arrangement and are promising NLO candidates. In the present work, a series of 15 donor-π-acceptor type vinyl coupled triazene derivatives (VCTDs) with different acceptors (-NO(2), -CN, and -COOH) have been designed, and their structure, nonlinear response, and optoelectronic properties have been studied using density functional theory and time-dependent density functional theory methods. B3LYP/6-311g(d,p) optimized geometries of the designed candidates show delocalization from the acceptor to donor through a π-bridge. Molecular orbital composition analysis reveals that HOMO is stabilized by the π-bridge, whereas acceptors play a major role in the stabilization of LUMO. Among the three acceptors, nitro derivatives are found to be efficient NLO candidates, and tri- and di-substituted cyano and carboxylic acid derivatives also show reasonably good NLO response. The effect of solvation on these properties has been studied using PCM calculations. From TDDFT calculations, the computed absorption spectra of these candidates lie in the range of 350-480 nm in the gas phase and have positive solvatochromism. The ground-state stabilization interactions are accounted from NBO calculations. In an effort to substantiate the thermal stability of the designed candidates, computations have been done to identify the weak interactions in the systems through NCI and AIM analysis. In summary, 10 out of 15 designed candidates are found to have excellent NLO and optoelectronic properties.

Metal-promoted restoration of defective graphene

A novel metal-participating rearrangement mechanism of graphene is elucidated via density functional calculations. Results show that the barrier for the elimination of Stone–Wales defects can be decreased by the adsorbed transition metal atoms. Molecular orbital composition analysis shows that the contribution from the metal atom to the frontier orbital in the transition state is a key factor for the distinct metal catalytic properties. Among the chosen elements (Cu, Ni, Fe, Cr, Mo, and W), tungsten can reduce the activation energy remarkably from 6.2 to 2.9 eV, and 1000 K is regarded as a favorable temperature to yield perfect hexagonal nanographene. In contrast to curved network structures in fullerenes and carbon nanotubes, the open and planar structure of graphene helped to accommodate kinetic transformations of the carbon skeleton and metal atoms in favorable pathways.