Seal Formation in Silicon Planar Patch-Clamp Microstructures

This paper presents a microfabricated planar patch-clamp electrode design and looks at the impact of several physical characteristics on seal formation. The device consists of a patch aperture, 1.5-2.5 mum in diameter and 7-12 mum in depth, with a reverse-side deep-etched 80-mum well. The patch aperture was coated with either thermal oxide or plasma-enhanced chemical vapor deposited (PECVD) SiO2. Some of the thermal oxide devices were converted into protruding nozzle structures, and some were boron-doped. Seal formation was tested with cultured N2a neuroblastoma cells. The PECVD oxide devices produced an average seal resistance of 34 MOmega(n = 24), and the thermal oxide devices produced an average seal resistance of 96 MOmega(n = 59). Seal resistance was found to positively correlate with patch aperture depth. Whole-cell recordings were obtained from 14% of cells tested with the thermal oxide devices, including a single recording where a gigaohm seal was obtained.

First human hNT astrocytes patterned to single cell resolution on parylene-C/Silicon dioxide substrates

In our previous work we developed a successful protocol to pattern the human hNT neuron (derived from the human teratocarcinoma cell line (hNT)) on parylene-C/SiO2 substrates. This communication, reports how we have successfully managed to pattern the supportive cell to the neuron, the hNT astrocyte, on such substrates. Here we disseminate the nanofabrication, cell differentiation and cell culturing protocols necessary to successfully pattern the first human hNT astrocytes to single cell resolution on parylene-C/SiO2 substrates. This is performed for varying parylene strip widths providing excellent contrast to the SiO2 substrate and elegant single cell isolation at 10μm strip widths. The breakthrough in patterning human cells on a silicon chip has widespread implications and is valuable as a platform technology as it enables a detailed study of the human brain at the cellular and network level.

On the difficulties of present theoretical models to predict the oxidation state of atomic Au adsorbed on regular sites of CeO2(111)

The electronic structure and oxidation state of atomic Au adsorbed on a perfect CeO2(111) surface have been investigated in detail by means of periodic density functional theory-based calculations, using the LDA+U and GGA+U potentials for a broad range of U values, complemented with calculations employing the HSE06 hybrid functional. In addition, the effects of the lattice parameter a0 and of the starting point for the geometry optimization have also been analyzed. From the present results we suggest that the oxidation state of single Au atoms on CeO2(111) predicted by LDA+U, GGA+U, and HSE06 density functional calculations is not conclusive and that the final picture strongly depends on the method chosen and on the construction of the surface model. In some cases we have been able to locate two well-defined states which are close in energy but with very different electronic structure and local geometries, one with Au fully oxidized and one with neutral Au. The energy difference between the two states is typically within the limits of the accuracy of the present exchange-correlation potentials, and therefore, a clear lowest-energy state cannot be identified. These results suggest the possibility of a dynamic distribution of Au0 and Au+ atomic species at the regular sites of the CeO2(111) surface.

Detection of Oxidation Products of 5-Methyl-2′-Deoxycytidine in Arabidopsis DNA

Epigenetic regulations play important roles in plant development and adaptation to environmental stress. Recent studies from mammalian systems have demonstrated the involvement of ten-eleven translocation (Tet) family of dioxygenases in the generation of a series of oxidized derivatives of 5-methylcytosine (5-mC) in mammalian DNA. In addition, these oxidized 5-mC nucleobases have important roles in epigenetic remodeling and aberrant levels of 5-hydroxymethyl-29-deoxycytidine (5-HmdC) were found to be associated with different types of human cancers. However, there is a lack of evidence supporting the presence of these modified bases in plant DNA. Here we reported the use of a reversed-phase HPLC coupled with tandem mass spectrometry method and stable isotope-labeled standards for assessing the levels of the oxidized 5-mC nucleosides along with two other oxidatively induced DNA modifications in genomic DNA of Arabidopsis. These included 5- HmdC, 5-formyl-29-deoxycytidine (5-FodC), 5-carboxyl-29-deoxycytidine (5-CadC), 5-hydroxymethyl-29-deoxyuridine (5- HmdU), and the (59S) diastereomer of 8,59-cyclo-29-deoxyguanosine (S-cdG). We found that, in Arabidopsis DNA, the levels of 5-HmdC, 5-FodC, and 5-CadC are approximately 0.8 modifications per 106 nucleosides, with the frequency of 5-HmdC (per 5-mdC) being comparable to that of 5-HmdU (per thymidine). The relatively low levels of the 5-mdC oxidation products suggest that they arise likely from reactive oxygen species present in cells, which is in line with the lack of homologous Tetfamily dioxygenase enzymes in Arabidopsis.

Ozonolysis of methyl oleate monolayers at the air–water interface: oxidation kinetics, reaction products and atmospheric implications

Ozonolysis of methyl oleate monolayers at the air–water interface results in surprisingly rapid loss of material through cleavage of the C[double bond, length as m-dash]C bond and evaporation/dissolution of reaction products. We determine using neutron reflectometry a rate coefficient of (5.7 ± 0.9) × 10−10 cm2 molecule−1 s−1 and an uptake coefficient of [similar]3 × 10−5 for the oxidation of a methyl ester monolayer: the atmospheric lifetime is [similar]10 min. We obtained direct experimental evidence that <2% of organic material remains at the surface on atmospheric timescales. Therefore known long atmospheric residence times of unsaturated fatty acids suggest that these molecules cannot be present at the interface throughout their ageing cycle, i.e. the reported atmospheric longevity is likely to be attributed to presence in the bulk and viscosity-limited reactive loss. Possible reaction products were characterized by ellipsometry and uncertainties in the atmospheric fate of organic surfactants such as oleic acid and its methyl ester are discussed. Our results suggest that a minor change to the structure of the molecule (fatty acid vs. its methyl ester) considerably impacts on reactivity and fate of the organic film.

Thiocyanate complexes of uranium in multiple oxidation states: a combined structural, magnetic, spectroscopic, spectroelectrochemical, and theoretical study

A comprehensive study of the complexes A4[U(NCS)8] (A = Cs, Et4N, nBu4N) and A3[UO2(NCS)5] (A = Cs, Et4N) is described, with the crystal structures of [nBu4N]4[U(NCS)8]·2MeCN and Cs3[UO2(NCS)5]·O0.5 reported. The magnetic properties of square antiprismatic Cs4[U(NCS)8] and cubic [Et4N]4[U(NCS)8] have been probed by SQUID magnetometry. The geometry has an important impact on the low-temperature magnetic moments: at 2 K, μeff = 1.21 μB and 0.53 μB, respectively. Electronic absorption and photoluminescence spectra of the uranium(IV) compounds have been measured. The redox chemistry of [Et4N]4[U(NCS)8] has been explored using IR and UV–vis spectroelectrochemical methods. Reversible 1-electron oxidation of one of the coordinated thiocyanate ligands occurs at +0.22 V vs Fc/Fc+, followed by an irreversible oxidation to form dithiocyanogen (NCS)2 which upon back reduction regenerates thiocyanate anions coordinating to UO22+. NBO calculations agree with the experimental spectra, suggesting that the initial electron loss of [U(NCS)8]4– is delocalized over all NCS– ligands. Reduction of the uranyl(VI) complex [Et4N]3[UO2(NCS)5] to uranyl(V) is accompanied by immediate disproportionation and has only been studied by DFT methods. The bonding in [An(NCS)8]4– (An = Th, U) and [UO2(NCS)5]3– has been explored by a combination of DFT and QTAIM analysis, and the U–N bonds are predominantly ionic, with the uranyl(V) species more ionic that the uranyl(VI) ion. Additionally, the U(IV)–NCS ion is more ionic than what was found for U(IV)–Cl complexes.

Serum protein layers on parylene-C and silicon oxide: effect on cell adhesion

Among the range of materials used in bioengineering, parylene-C has been used in combination with silicon oxide and in presence of the serum proteins, in cell patterning. However, the structural properties of adsorbed serum proteins on these substrates still remain elusive. In this study, we use an optical biosensing technique to decipher the properties of fibronectin (Fn) and serum albumin adsorbed on parylene-C and silicon oxide substrates. Our results show the formation of layers with distinct structural and adhesive properties. Thin, dense layers are formed on parylene-C, whereas thicker, more diffuse layers are formed on silicon oxide. These results suggest that Fn acquires a compact structure on parylene-C and a more extended structure on silicon oxide. Nonetheless, parylene-C and silicon oxide substrates coated with Fn host cell populations that exhibit focal adhesion complexes and good cell attachment. Albumin adopts a deformed structure on parylene-C and a globular structure on silicon oxide, and does not support significant cell attachment on either surface. Interestingly, the co-incubation of Fn and albumin at the ratio found in serum, results in the preferential adsorption of albumin on parylene-C and Fn on silicon oxide. This finding is supported by the exclusive formation of focal adhesion complexes in differentiated mouse embryonic stem cells (CGR8), cultured on Fn/albumin coated silicon oxide, but not on parylene-C. The detailed information provided in this study on the distinct properties of layers of serum proteins on substrates such as parylene-C and silicon oxide is highly significant in developing methods for cell patterning.

Reversal of a single base pair step controls guanine photo-oxidation by an intercalating Ru(II) dipyridophenazine complex

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo-oxidation by Λ [Ru(TAP)2(dppz)]2+ have been compared in 5′-{CCGGATCCGG}2 and 5′-{CCGGTACCGG}2 using ps/ns transient visible and time-resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′-TA-3′ vs. 5′-AT-3′ binding preference predicted by X-ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.

Modeling the photo-oxidation of dissolved organic matter by ultraviolet radiation in freshwater lakes: implications for mercury bioavailability

Uncertainties in projected ultraviolet (UV) radiation may lead to future increases in UV irradiation of freshwater lakes. Because dissolved organic carbon (DOC) is the main binding phase for mercury (Hg) in freshwater lakes, an increase in DOC photo-oxidation may affect Hg speciation and bioavailability. We quantified the effect of DOC concentration on the rate of abiotic DOC photo-oxidation for five lakes (DOC = 3.27–12.3 mg L−1) in Kejimkujik National Park, Canada. Samples were irradiated with UV-A or UV-B radiation over a 72-h period. UV-B radiation was found to be 2.36 times more efficient at photo-oxidizing DOC than UV-A, with energy-normalized rates of dissolved inorganic carbon (DIC) production ranging from 3.8 × 10−5 to 1.1 × 10−4 mg L−1 J−1 for UV-A, and from 6.0 × 10−5 to 3.1 × 10−4 mg L−1 J−1 for UV-B. Energy normalized rates of DIC production were positively correlated with DOC concentrations. Diffuse integrated attenuation coefficients were quantified in situ (UV-A Kd = 0.056–0.180 J cm−1; UV-B Kd = 0.015–0.165 J cm−1) and a quantitative depth-integrated model for yearly DIC photo-production in each lake was developed. The model predicts that, UV-A produces between 3.2 and 100 times more DIC (1521–2851 mg m−2 year−1) than UV-B radiation (29.17–746.7 mg m−2 year−1). Future increases in UV radiation may increase DIC production and increase Hg bioavailability in low DOC lakes to a greater extent than in high DOC lakes.

Monitoring guanine photo-oxidation by enantiomerically resolved Ru(II) dipyridophenazine complexes using inosine-substituted oligonucleotides

The intercalating [Ru(TAP)2(dppz)]2+ complex can photo-oxidise guanine in DNA, although in mixed-sequence DNA it can be difficult to understand the precise mechanism due to uncertainties in where and how the complex is bound. Replacement of guanine with the less oxidisable inosine (I) base can be used to understand the mechanism of electron transfer (ET). Here the ET has been compared for both L- and D-enantiomers of [Ru(TAP)2(dppz)]2+ in a set of sequences where guanines in the readily oxidisable GG step in {TCGGCGCCGA}2 have been replaced with I. The ET has been monitored using picosecond and nanosecond transient absorption and ps-time-resolved IR spectroscopy. In both cases inosine replacement leads to a diminished yield, but the trends are strikingly different for L- and D-complexes.

Caesalpinia decapetala extracts as inhibitors of lipid oxidation in beef patties

In this study we investigated the effects of Caesalpinia decapetala (CD) extracts on lipid oxidation in ground beef patties. Plant extracts and butylated hydroxytoluene (BHT) were individually added to patties at both 0.1% and 0.5% (w/w) concentrations. We assessed the antioxidant efficacy of CD by the ferric reducing antioxidant power (FRAP) assay and evaluated their potential as natural antioxidants for meat preservation by thiobarbituric acid reactive substance (TBARS) values, hexanal content, fatty acid composition and color parameters. These were tested periodically during 11 days of refrigerated storage. TBARS levels were significantly lower (p ≤ 0.05) in the samples containing plant extracts or BHT than in the non-treated control. In addition, the beef patties formulated with the selected plant extracts showed significantly (p ≤ 0.05) better color stability than those without antioxidants. These results indicate that edible plant extracts are promising sources of natural antioxidants and can potentially be used as functional preservatives in meat products.

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl–DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

Role of ligands in catalytic water oxidation by mononuclear ruthenium complexes

Since first reported in 2005, mononuclear ruthenium water oxidation catalysts have attracted a great deal of attention due to their catalytic performance and synthetic flexibility. In particular, ligands coordinated to a Ru metal centre play an important role in the catalytic mechanisms, exhibiting significant impact on catalyst efficiency, stability and activity towards water oxidation. This review focuses on finding possible correlations between the ligand effects and activity of mononuclear Ru aqua and non-aqua complexes as water oxidation catalysts. The ligand effects highlighted in the text include the electronic nature of core ligands and their substituents, the trans–cis effect, steric hindrance and the strain effect, the net charge effect, the geometric arrangement of the aqua ligand and the supramolecular effects, e.g., hydrogen bonding and influence of a pendant base. The outcome is not always obvious at the present knowledge level. Deeper understanding of the ligand effects, based on new input data, is mandatory for further progress towards a rational development of novel catalysts featuring enhanced activity in water oxidation.

The partial oxidation of methane over Pd/Al2O3 catalyst nanoparticles studied in-situ by near ambient-pressure x-ray photoelectron spectroscopy

Near ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) is used to study the chemical state of methane oxidation catalysts in-situ. Al2O3{supported Pd catalysts are prepared with different particle sizes ranging from 4 nm to 10 nm. These catalysts were exposed to conditions similar to those used in the partial oxidation of methane (POM) to syn-gas and simultaneously monitored by NAP-XPS and mass spectrometry. NAP-XPS data show changes in the oxidation state of the palladium as the temperature in- creases, from metallic Pd0 to PdO, and back to Pd0. Mass spectrometry shows an increase in CO production whilst the Pd is in the oxide phase, and the metal is reduced back under presence of newly formed H2. A particle size effect is observed, such that CH4 conversion starts at lower temperatures with larger sized particles from 6 nm to 10 nm. We find that all nanoparticles begin CH4 conversion at lower temperatures than polycrystalline Pd foil.

Asymmetric oxidation of vinyl- and ethynyl terthiophene ligands in triruthenium complexes

A series of ruthenium(II) complexes [{RuCl(CO)(PMe3)3(–CHvCH–)}nX], 1a–1c (1a: n = 3, X = 3,3’’- dimethyl-2,2’:3’,2’’-terthiophene; 1b: n = 2, X = 2,2’-bithiophene; 1c: n = 2, X = 2,3-bis(3-methylthiophen- 2-yl)benzothiophene) and [{Cp*(dppe)2Ru(–CuC–)}3X], 1d (X = 3,3’’-dimethyl-2,2’:3’,2’’- terthiophene), were prepared and characterized by 1H, 13C and 31P NMR. Their redox, spectroscopic and bonding properties were studied with a range of spectro-electrochemical methods in combination with density functional theory calculations. The first two anodic steps observed for 1a and 1d are largely localized on the lateral frameworks of the molecular triangle, the direct conjugation between them being precluded due to the photostable open form of the dithienyl ethene moiety. The third anodic step is then mainly localized on the centerpiece of the triangular structure, affecting both bithiophene laterals. The experimental IR and UV-vis-NIR spectroelectrochemical data and, largely, also DFT calculations account for this explanation, being further supported by direct comparison with the anodic behavior of reference diruthenium complexes 1b and 1c.