Complex Chemical Environment Research Articles

The effect of EPA and DHA on platelets treated with multiple agonists found in the thrombus core (671.3)

The omega‐3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been consistently associated with reduced platelet function, and more recently, with impaired thrombin generation. However, almost all studies to date have focused on how EPA and DHA alter platelet physiology in response to monotypic agonist stimulation. This reductionist approach does not recapitulate the complex chemical environment found in a developing thrombus. Therefore, we asked if platelets treated with multiple agonists like those found in the thrombus core would also display EPA and DHA‐mediated inhibition. We found that optical aggregometry and dense granule secretion was diminished after EPA and DHA incorporation in platelets stimulated with the core clot agonists. We also noted a reduction in both the protein content of platelet lipid rafts and thrombin generation after core agonist stimulation, consistent with our earlier observations. Transmission electron micrographic imaging also established that EPA and DHA‐treated platelets showed moderate ultrastructural malformations after core agonist treatment. These results all suggest that EPA and DHA can abrogate platelet signaling responses within the core of a developing thrombus, further illustrating the potential health benefits of increased EPA and DHA intake.Grant Funding Source: Supported by an Institutional Development Award (IDeA) from the NIH/NIGMS, #P20GM103443

Improved Design of Sensitive Diathermancy and Application in High Accuracy Chemical Unite Operation

The high accuracy of heat inspect system was very important for the use of accuracy control in the chemical industry. The difficult of high accuracy of heat inspect system was how to get the heat information with high accuracy and control the system at real time. In traditional method, the linear system was used to control the feedback of the heat, with the data sampled discrete, the model-based heat inspect of chemical industry was easily influenced by modeling errors and disturbances of complex chemical environment, which cause underreporting or false alarms, the result was not good. So a high accuracy application of sensitive diathermancy design method was proposed and applied in high accuracy chemical unite operation and chemical industry, a heat inspect method of principal component cluster analysis for the chemical industry, the accurate diathermancy heat inspect data was sampled with many sensitive diathermancy in different location, the corresponding heat inspect signal through effective heat inspect method was analyzed to deter the corresponding chemical diathermancy was faulty, with the data fusion method, the accurate data was output to control the system. Simulation results show that with sensitive diathermancy used in chemical unit operation, the heat data is outputted with high accuracy, and it has good application value in chemical industry.

Headspace analysis of new psychoactive substances using a Selective Reagent Ionisation-Time of Flight-Mass Spectrometer

The rapid expansion in the number and use of new psychoactive substances presents a significant analytical challenge because highly sensitive instrumentation capable of detecting a broad range of chemical compounds in real-time with a low rate of false positives is required. A Selective Reagent Ionisation-Time of Flight-Mass Spectrometry (SRI-ToF-MS) instrument is capable of meeting all of these requirements. With its high mass resolution (up to m/Δm of 8000), the application of variations in reduced electric field strength (E/N) and use of different reagent ions, the ambiguity of a nominal (monoisotopic) m/z is reduced and hence the identification of chemicals in a complex chemical environment with a high level of confidence is enabled. In this study we report the use of a SRI-ToF-MS instrument to investigate the reactions of H3O+, O2+, NO+ and Kr+ with 10 readily available (at the time of purchase) new psychoactive substances, namely 4-fluoroamphetamine, methiopropamine, ethcathinone, 4-methylethcathinone, N-ethylbuphedrone, ethylphenidate, 5-MeO-DALT, dimethocaine, 5-(2-aminopropyl)benzofuran and nitracaine. In particular, the dependence of product ion branching ratios on the reduced electric field strength for all reagent ions was investigated and is reported here. The results reported represent a significant amount of new data which will be of use for the development of drug detection techniques suitable for real world scenarios.

First principles calculation of inhomogeneous broadening in solid-state cw-EPR spectroscopy

We present a scheme for the first-principles calculation of EPR lineshapes for continuous-wave-EPR spectroscopy (cw-EPR) of spin centers in complex chemical environments. We specifically focus on poorly characterized systems, e.g. powders and frozen glasses with variable microsolvation structures. Our approach is based on ab initio molecular dynamics simulations and ab initio calculations of the ensemble of g- and A-tensors along the trajectory. The method incorporates temperature effects as well as the full anharmonicity of the intra- and intermolecular degrees of freedom of the system. We apply this scheme to compute the lineshape of a prototypical spin probe, the nitrosodisulfonate dianionic radical (Fremy's salt), dissolved in a 50 : 50 mixture of water and methanol. We are able to determine the specific effect of variations of local solvent composition and microsolvation structure on the cw-EPR lineshape. Our molecular dynamics reveal a highly anisotropic solvation structure with distinct spatial preferences for water and methanol around Fremy's salt that can be traced back to a combination of steric and polar influences. The overall solvation structure and conformational preferences of Fremy's salt as found in our MD simulations agree very well with the results obtained from EPR and orientation-selective ENDOR spectroscopy performed on the frozen glass. The simulated EPR lineshapes show good agreement with the experimental spectra. When combined with our MD results, they characterize the lineshape dependence on local morphological fluctuations.

Mechanisms of Development and Evolution of the Insect Olfactory System

To increase detection of a complex chemical environment, vertebrates and insects express an extraordinary number of distinct olfactory receptor neuron (ORN) classes, each functionally specialized to detect a set of odorants. This is achieved as the olfactory system develops and each of these ORN classes makes developmental decisions defining the olfactory receptor genes they will express and their class-specific connections in the brain. In addition to this high level of ORN diversity, olfactory systems are also very dynamic evolutionarily, with both the number and functionality of olfactory receptor genes as well as the requirement for certain ORN circuits being under ecological constraints. In this review, we will discuss molecular and developmental strategies underlying ORN diversity and evolutionary plasticity as well as present the insect olfactory system as a model for evo-devo research in light of recent findings.

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

Density functional theory was employed to study the influence of O-phosphorylation of serine, threonine, and tyrosine on the amidic (15)N chemical shielding anisotropy (CSA) tensor in the context of the complex chemical environments of protein structures. Our results indicate that the amidic (15)N CSA tensor has sensitive responses to the introduction of the phosphate group and the phosphorylation-promoted rearrangement of solvent molecules and hydrogen bonding networks in the vicinity of the phosphorylated site. Yet, the calculated (15)N CSA tensors in phosphorylated model peptides were in range of values experimentally observed for non-phosphorylated proteins. The extent of the phosphorylation induced changes suggests that the amidic (15)N CSA tensor in phosphorylated proteins could be reasonably well approximated with averaged CSA tensor values experimentally determined for non-phosphorylated amino acids in practical NMR applications, where chemical surrounding of the phosphorylated site is not known a priori in majority of cases. Our calculations provide estimates of relative errors to be associated with the averaged CSA tensor values in interpretations of NMR data from phosphorylated proteins.

Hydrodynamic modulation of pluripotent stem cells

Controlled expansion and differentiation of pluripotent stem cells (PSCs) using reproducible, high-throughput methods could accelerate stem cell research for clinical therapies. Hydrodynamic culture systems for PSCs are increasingly being used for high-throughput studies and scale-up purposes; however, hydrodynamic cultures expose PSCs to complex physical and chemical environments that include spatially and temporally modulated fluid shear stresses and heterogeneous mass transport. Furthermore, the effects of fluid flow on PSCs cannot easily be attributed to any single environmental parameter since the cellular processes regulating self-renewal and differentiation are interconnected and the complex physical and chemical parameters associated with fluid flow are thus difficult to independently isolate. Regardless of the challenges posed by characterizing fluid dynamic properties, hydrodynamic culture systems offer several advantages over traditional static culture, including increased mass transfer and reduced cell handling. This article discusses the challenges and opportunities of hydrodynamic culture environments for the expansion and differentiation of PSCs in microfluidic systems and larger-volume suspension bioreactors. Ultimately, an improved understanding of the effects of hydrodynamics on the self-renewal and differentiation of PSCs could yield improved bioprocessing technologies to attain scalable PSC culture strategies that will probably be requisite for the development of therapeutic and diagnostic applications.

Graphene-Based Aptamer Logic Gates and Their Application to Multiplex Detection

In this work, a GO/aptamer system was constructed to create multiplex logic operations and enable sensing of multiplex targets. 6-Carboxyfluorescein (FAM)-labeled adenosine triphosphate binding aptamer (ABA) and FAM-labeled thrombin binding aptamer (TBA) were first adsorbed onto graphene oxide (GO) to form a GO/aptamer complex, leading to the quenching of the fluorescence of FAM. We demonstrated that the unique GO/aptamer interaction and the specific aptamer-target recognition in the target/GO/aptamer system were programmable and could be utilized to regulate the fluorescence of FAM via OR and INHIBIT logic gates. The fluorescence changed according to different input combinations, and the integration of OR and INHIBIT logic gates provided an interesting approach for logic sensing applications where multiple target molecules were present. High-throughput fluorescence imagings that enabled the simultaneous processing of many samples by using the combinatorial logic gates were realized. The developed logic gates may find applications in further development of DNA circuits and advanced sensors for the identification of multiple targets in complex chemical environments.

Insights from theoretical calculations on structure, dynamics, phase behavior and hydrogen sorption in nanoporous metal organic frameworks

Metal organic framework (MOF) materials are gaining lot of interest because of their potential as hydrogen storage materials. Due to their nanosize, understanding hydrogen sorption behavior, structural flexibility, phase behavior, etc. is difficult to study by experimental methods. In this situation, various levels of theoretical calculations have provided us with invaluable insights about these materials. However, applying a general theory may not work for these materials due to their complex chemical environment. Thus, modification to the existing theory, developing new potential, and parameterization of force field has been a focus for theoreticians working in this area. In this review we have summarized these theories and the specific requirements that have been instrumental in studying hydrogen sorption in MOFs and their physicochemical properties and present the current knowledge about these materials. We also provide various physical chemical aspects to achieve high hydrogen sorption capacity in MOF materials.

The interplay of catechol ligands with nanoparticulate iron oxides

The unique properties exhibited by nanoscale materials, coupled with the multitude of chemical surface derivatisation possibilities, enable the rational design of multifunctional nanoscopic devices. Such functional devices offer exciting new opportunities in medical research and much effort is currently invested in the area of "nanomedicine", including: multimodal imaging diagnostic tools, platforms for drug delivery and vectorisation, polyvalent, multicomponent vaccines, and composite devices for "theranostics". Here we will review the surface derivatisation of nanoparticulate oxides of iron and iron@iron-oxide core-shells. They are attractive candidates for MRI-active therapeutic platforms, being potentially less toxic than lanthanide-based materials, and amenable to functionalisation with ligands. However successful grafting of groups onto the surface of iron-based nanoparticles, thus adding functionality whilst preserving their inherent properties, is one of the most difficult challenges for creating truly useful nanodevices from them. Functionalised catechol-derived ligands have enjoyed success as agents for the masking of superparamagnetic iron-oxide particles, often so as to render them biocompatible with medium to long-term colloidal stability in the complex chemical environments of biological milieux. In this perspective, the opportunities and limitations of functionalising the surfaces of iron-oxide nanoparticles, using coatings containing a catechol-derived anchor, are analysed and discussed, including recent advances using dopamine-terminated stabilising ligands. If light-driven ligand to metal charge transfer (LMCT) processes, and pH-dependent ligand desorption, leading to nanoparticle degradation under physiologically relevant conditions can be suppressed, colloidal stability of samples can be maintained and toxicity ascribed to degradation products avoided. Modulation of the redox behaviour of iron catecholate systems through the introduction of an electron-withdrawing substituent to the aromatic π-system of the catechol is a promising approach towards achieving these goals.

Comparative structural bioinformatics analysis of Bacillus amyloliquefaciens chemotaxis proteins within Bacillus subtilis group

Chemotaxis is a process in which bacteria sense their chemical environment and move towards more favorable conditions. Since plant colonization by bacteria is a multifaceted process which requires a response to the complex chemical environment, a finely tuned and sensitive chemotaxis system is needed. Members of the Bacillus subtilis group including Bacillus amyloliquefaciens are industrially important, for example, as bio-pesticides. The group exhibits plant growth-promoting characteristics, with different specificity towards certain host plants. Therefore, we hypothesize that while the principal molecular mechanisms of bacterial chemotaxis may be conserved, the bacterial chemotaxis system may need an evolutionary tweaking to adapt it to specific requirements, particularly in the process of evolution of free-living soil organisms, towards plant colonization behaviour. To date, almost nothing is known about what parts of the chemotaxis proteins are subjected to positive amino acid substitutions, involved in adjusting the chemotaxis system of bacteria during speciation. In this novel study, positively selected and purified sites of chemotaxis proteins were calculated, and these residues were mapped onto homology models that were built for the chemotaxis proteins, in an attempt to understand the spatial evolution of the chemotaxis proteins. Various positively selected amino acids were identified in semi-conserved regions of the proteins away from the known active sites.

Sensing properties of polyethylenimine coated carbon nanotubes in oxidized oil

Chemical detection is still a continuous challenge when it comes to designing single-walled carbon nanotube (SWCNT) sensors with high selectivity, especially in complex chemical environments. A perfect example of such an environment would be in thermally oxidized soybean oil. At elevated temperatures, oil oxidizes through a series of chemical reactions that results in the formation of monoacylglycerols, diacylglycerols, oxidized triacylglycerols, dimers, trimers, polymers, free fatty acids, ketones, aldehydes, alcohols, esters, and other minor products. In order to detect the rancidity of oxidized soybean oil, carbon nanotube chemiresistor sensors have been coated with polyethylenimine (PEI) to enhance the sensitivity and selectivity. PEI functionalized SWCNTs are known to have a high selectivity towards strong electron withdrawing molecules. The sensors were very responsive to different oil oxidation levels and furthermore, displayed a rapid recovery of more than 90% in ambient air without the need of heating or UV exposure.

Use of proton transfer reaction time-of-flight mass spectrometry for the analytical detection of illicit and controlled prescription drugs at room temperature via direct headspace sampling

The first reported use of proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) for the detection of a range of illicit and prescribed drugs is presented here. We describe the capabilities of PTR-TOF-MS to detect the following commonly used narcotics-ecstasy (N-methyl-3,4-methylenedioxyamphetamine), morphine, codeine, cocaine and heroin-by the direct sampling of the headspace above small solid quantities (approximately 50 mg) of the drugs placed in glass vials at room temperature, i.e. with no heating of the sample and no pre-concentration. We demonstrate in this paper the ability to identify the drugs, both illicit and prescribed, using PTR-TOF-MS through the accurate m/z assignment of the protonated parent molecule to the second decimal place. We have also included in this study measurements with an impure sample of heroin, containing typical substances found in "street" heroin, to illustrate the use of the technology for more "real-world" samples. Therefore, in a real-world complex chemical environment, a high level of confidence can be placed on the detection of drugs. Although the protonated parent is observed for all drugs, the reactant channel leading to this species is not the only one observed and neither is it necessarily the most dominant. Details on the observed fragmentation behaviour are discussed and compared to electrospray ionisation MS(n) studies available in the literature.

Surface Chemistry in the Process of Coating Mesoporous SiO2 onto Carbon Nanotubes Driven by the Formation of SiOC Bonds

The deposition of mesoporous silica (SiO(2)) on carbon nanotubes (CNTs) has opened up a wide range of assembling possibilities by exploiting the sidewall of CNTs and organosilane chemistry. The resulting systems may be suitable for applications in catalysis, energy conversion, environmental chemistry, and nanomedicine. However, to promote the condensation of silicon monomers on the nanotube without producing segregated particles, (OR)(4-x)SiO(x)(x-) units must undergo nucleophilic substitution by groups localized on the CNT sidewall during the transesterification reaction. In order to achieve this preferential attachment, we have deposited silica on oxidized carbon nanotubes (single-walled and multiwalled) in a sol-gel process that also involved the use of a soft template (cetyltrimethylammonium bromide, CTAB). In contrast to the simple approach normally used to describe the attachment of inorganic compounds on CNTs, SiO(2) nucleation on the tube is a result of nucleophilic attack mainly by hydroxyl radicals, localized in a very complex surface chemical environment, where various oxygenated groups are covalently bonded to the sidewall and carboxylated carbonaceous fragments (CCFs) are adsorbed on the tubes. Si-O-C covalent bond formation in the SiO(2)-CNT hybrids was observed even after removal of the CCFs with sodium hydroxide. By adding CTAB, and increasing the temperature, time, and initial amount of the catalyst (NH(4)OH) in the synthesis, the SiO(2) coating morphology could be changed from one of nanoparticles to mesoporous shells. Concomitantly, pore ordering was achieved by increasing the amount of CTAB. Furthermore, preferential attachment on the sidewall results mostly in CNTs with uncapped ends, having sites (carboxylic acids) that can be used for further localized reactions.

Proton transfer reaction mass spectrometry for the sensitive and rapid real-time detection of solid high explosives in air and water

Relying on recent developments in proton transfer reaction mass spectrometry (PTR-MS), we demonstrate here the capability of detecting solid explosives in air and in water in real time. Two different proton transfer reaction mass spectrometers have been used in this study. One is the PTR-TOF 8000, which has an enhanced mass resolution (m/Δm up to 8,000) and high sensitivity (~50 cps/ppbv). The second is the high-sensitivity PTR-MS, which has an improved limit of detection of about several hundreds of parts per quadrillion by volume and is coupled with a direct aqueous injection device. These instruments have been successfully used to identify and monitor the solid explosive 2,4,6-trinitrotoluene (TNT) by analysing on the one hand the headspace above small quantities of samples at room temperature and from trace quantities not visible to the naked eye placed on surfaces (also demonstrating the usefulness of a simple pre-concentration and thermal desorption technique) and by analysing on the other hand trace compounds in water down to a level of about 100 pptw. The ability to identify even minute amounts of threat compounds, such as explosives, particularly within a complex chemical environment, is vital to the fight against crime and terrorism and is of paramount importance for the appraisal of the fate and harmful effects of TNT at marine ammunition dumping sites and the detection of buried antipersonnel and antitank landmines.

Ab initio study of thermodynamic, structural, and elastic properties of Mg-substituted crystalline calcite

Arthropoda, which represent nearly 80% of all known animal species, are protected by an exoskeleton formed by their cuticle. The cuticle represents a hierarchically structured multifunctional biocomposite based on chitin and proteins. Some groups, such as Crustacea, reinforce the load-bearing parts of their cuticle with calcite. As the calcite sometimes contains Mg it was speculated that Mg may have a stiffening impact on the mechanical properties of the cuticle (Becker et al., Dalton Trans. (2005) 1814). Motivated by these facts, we present a theoretical parameter-free quantum-mechanical study of the phase stability and structural and elastic properties of Mg-substituted calcite crystals. The Mg-substitutions were chosen as examples of states that occur in complex chemical environments typical for biological systems in which calcite crystals contain impurities, the role of which is still the topic of debate. Density functional theory calculations of bulk (Ca,Mg)CO₃ were performed employing 30-atom supercells within the generalized gradient approximation as implemented in the Vienna Ab-initio Simulation Package. Based on the calculated thermodynamic results, low concentrations of Mg atoms are predicted to be stable in calcite crystals in agreement with experimental findings. Examining the structural characteristics, Mg additions nearly linearly reduce the volume of substituted crystals. The predicted elastic bulk modulus results reveal that the Mg substitution nearly linearly stiffens the calcite crystals. Due to the quite large size-mismatch of Mg and Ca atoms, Mg substitution results in local distortions such as off-planar tilting of the CO₃²⁻ group.

Inactivation of Vegetative and Sporulated Bacteria by Dry Gaseous Ozone

Inactivation by gaseous ozone of different types of microorganisms is successfully achieved provided, as is well known, the gaseous phase is strongly humidified. The inactivation mechanisms and species involved in this process are, however, not yet clearly identified. To gain insight, we considered exposure of bacterial spores to dry rather than humidified ozone, a less complex chemical environment. In contrast to most of the published literature, it is shown that, under strict dry ozone conditions, bacterial spores can be inactivated, but to a degree that is largely dependent on the spore type and substrate material. In this case, the O3 molecule is determined to be responsible for the inactivation process through its diffusion into and oxidative action within the spore, as no outer erosion of the spore is detected. With humidified ozone, a higher inactivation efficiency is observed that is most probably related, in part, to the swelling of the spore, which facilitates the diffusion of oxidative species within it and up to the core; besides O3, these oxidative agents stem from the interaction of O3 with H2O, which in the end leads to a heavily damaged spore structure, in contrast to dry-ozone exposure where the spore integrity is maintained.

Proton transfer reaction mass spectrometry investigations on the effects of reduced electric field and reagent ion internal energy on product ion branching ratios for a series of saturated alcohols

In this paper we report an investigation of the effects of E/ N over the range of 90–140 Td on the product ions resulting from the reactions of H 3O + with 12 saturated alcohols using a proton transfer reaction mass spectrometer (PTR-MS). The alcohols included in this study are methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-methyl-1-propanol, 2-methyl-2-propanol, 2-butanol, cyclopentanol, 1-pentanol, cyclohexanol, and 1-hexanol. Only in the cases of methanol and ethanol are any substantial amounts of the protonated parent observed at any E/ N. For the other saturated alcohols predominantly fragment ions are observed. This implies that attempts to identify and hence monitor saturated alcohols in trace concentrations in a complex chemical environment using PTR-MS will be fraught with difficulties because a given m/ z will not be unique to a particular chemical compound, i.e., multiple species could be present at a given m/ z. In addition to changes in E/ N we present preliminary results with regards to changing the conditions in the generation of the reagent ions via altering the operational conditions within the ion source (a hollow cathode). We present product ion branching ratios as a function of hollow cathode emission current for cyclohexanol, 1-propanol and 2-propanol at fixed E/ N. Although not part of the reaction chamber, we have found that changing the hollow cathode emission current results in modifications to the product ion branching ratios. We presume that these observed changes are a result of altering the internal energies of the reagent ions and thereby modify the reaction kinetics and dynamics occurring within the drift tube of a PTR-MS.

Windows to cell function and dysfunction: Signatures written in the boundary layers

The medium surrounding cells either in culture or in tissues contains a chemical mix varying with cell state. As solutes move in and out of the cytoplasmic compartment they set up characteristic signatures in the cellular boundary layers. These layers are complex physical and chemical environments the profiles of which reflect cell physiology and provide conduits for intercellular messaging. Here we review some of the most relevant characteristics of the extracellular/intercellular space. Our initial focus is primarily on cultured cells but we extend our consideration to the far more complex environment of tissues, and discuss how chemical signatures in the boundary layer can or may affect cell function. Critical to the entire essay are the methods used, or being developed, to monitor chemical profiles in the boundary layers. We review recent developments in ultramicro electrochemical sensors and tailored optical reporters suitable for the task in hand.

An immunomagnetic PCR signal amplification assay for sensitive detection of Staphylococcus aureus enterotoxins in foods.

Enterotoxigenic strains of Staphylococcus aureus produce a variety of heat-stable staphylococcal enterotoxins (SEs) that are a prevalent cause of food poisoning in the United States and other countries. Many immunological and biochemical assays often work well in buffer systems but are hindered when tested in the complex chemical environment of foods. To overcome these biases and improve the limits of detection, we implemented an immunomagnetic PCR signal amplification assay (iPCR-SA) for recovery and detection of SEA and SEB in foods. Anti-SEA or anti-SEB primary antibodies were coated onto COOH-modified magnetic beads using 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide reagent. Secondary antibodies were covalently linked to amino-modified reporter DNA oligonucleotides (563 bp) via the linker molecule succinimidyl-4[N-maleimidomethyl]-cyclohexane-1-carboxylate. An internal 159-bp portion of the reporter DNA retained by the captured toxin molecule was then amplified by real-time PCR. A semiautomated Bead Retriever proved extremely helpful in both the application of the conjugation chemistries and required washes and the recovery and washing of bead-conjugated toxin from tested food samples. The procedure was simple, and analyses were completed in 5 to 6 h. The assay was sufficiently robust that we were able to detect SEA and SEB in tryptic soy broth, milk, lemon cream pie, tuna salad, deli turkey, and ground turkey at levels as low as 7.5 fg/ml. SE was still detected at high sensitivity after heating in food samples for typical pasteurization or cooking regimens. Sensitivity was diminished only when samples were subjected to extreme heating.