Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum

Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) C-13-H-1] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a ``uniqueness score'' and a ``coverage score''. Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of deduttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMIR-based metabolomics data by reducing existing impediments.

Efficient and practical synthesis of modular chiral beta-organochalcogeno amines, ArYCH2CH(R)NH2, and single crystal structures of (S) - MsOCH2CH(Bz)NH3+ center dot Cl- and (R)-MsOCH2CH(Ph)NH3+ center dot Cl-

Modular chiral I3-organochalcogeno amines, ArYCH2CH(R)NH2 (4a-4g) where R = Me, Bz, Ph; and ArY = PhS, BzSe and 4-MeOC6H4Te respectively have been synthesized and characterized. Compounds 4a-4g were synthesized (Method II) from chiral aminoalkyl 13-methanesulfonate hydrochlorides, MsOCH2CH(R)NH3+ center dot Cl- (2a-2c) through nucleophilic displacement of MsO- with organochalcogenolate (ArY-). In another attempt (Method I) chiral beta-organotelluro amines (4a-4c) were prepared by deprotection of chiral N-boc I3-organotelluro amides, 4-MeOC6H4TeCH2CH(R)NH-Boc (3a-3c), which in turn, 13,-,1 were made from chiral N-boc 13-methanesulfonate amides (la-lc) and ArTeNa. 1H, and FTIR spectra of all the compounds (3a-3c and 4a-4g) were characteristic. The composition of 3a-3c was determined by elemental analysis. The a]TD values of 3b-3c and 4a-4g were determined. The single crystal structures of (S)-2b and (R)-2c were determined by X-Ray diffraction studies. Both (S)-2b and (R)2c were crystallized in orthorhombic system and the Flack parameter x was found 0.08(12) and 0.00(2) respectively. The crystal of (S)-2b contain two asymmetric units with gauche (A) and staggered (B) conformations. There are NH Cl-, NH-O and CH-O intra and intermolecular secondary interactions in (S)-2b and (R)-2c resulting in supramolecular structures. (C) 2015 Elsevier By. All rights reserved.

Microhardness Studies of Vapour Grown Tin (II) Sulfide Single Crystals

Earth abundant tin sulfide (SnS) has attracted considerable attention as a possible absorber material for low-cost solar cells due to its favourable optoelectronic properties. Single crystals of SnS were grown by physical vapour deposition (PVD) technique. Microindentation studies were carried out on the cleaved surfaces of the crystals to understand their mechanical behaviour. Microhardness increased initially with the load, giving sharp maximum at 15 g. Quenching effect has increased the microhardness, while annealing reduced the microhardness of grown crystals. The hardness values of as-grown, annealed and quenched samples at 15 g load are computed to be 99.69, 44.52 and 106.29 kg/mm(2) respectively. The microhardness of PVD grown crystals are high compared to CdTe, a leading low-cost PV material. The as-grown faces are found to be fracture resistant.

Size Effects on Strength in the Transition from Single-to-Polycrystalline Behavior

During the transition from single crystalline to polycrystalline behavior, the available data show the strength increasing or decreasing as the number of grains in a cross section is reduced. Tensile experiments were conducted on polycrystalline Ni with grain sizes (d) between 16 and 140 mu m and varying specimen thickness (t), covering a range of lambda (-t/d) between similar to 0.5 and 20. With a decrease in lambda, the data revealed a consistent trend of strength being independent of lambda at large lambda, an increase in strength, and then a decrease in strength. Microstructural studies revealed that lower constraints enabled easier rotation of the surface grains and texture evolution, independent of the specimen thickness. In specimen interiors, there was a greater ease of rotation in thinner samples. Measurements of misorientation deviations within grains revealed important differences in the specimen interiors. A simple model is developed taking into account the additional geometrically necessary dislocations due to variations in the behavior of surface and interior grains, leading to additional strengthening. A suitable combination of this strengthening and surface weakening can give rise to wide range of possibilities with a decrease in lambda, including weakening, strengthening, and strengthening and weakening.

Functional roles of N-terminal and C-terminal domains in the overall activity of a novel single-stranded DNA binding protein of Deinococcus radiodurans

Single-stranded DNA binding protein (Ssb) of Deinococcus radiodurans comprises N- and C-terminal oligonucleotide/oligosaccharide binding (OB) folds connected by a beta hairpin connector. To assign functional roles to the individual OB folds, we generated three Ssb variants: Ssb(N) (N-terminal without connector), Ssb(NC) (N-terminal with connector) and Ssb(C) (C-terminal), each harboring one OB fold. Both Ssb(N) and Ssb(NC) displayed weak single-stranded DNA (ssDNA) binding activity, compared to the full-length Ssb (Ssb(FL)). The level of ssDNA binding activity displayed by SsbC was intermediate between Ssb(FL) and Ssb(N). Ssb(C) and Ssb(FL) predominantly existed as homo-dimers while Ssb(NC)/Ssb(N) formed different oligomeric forms. In vitro, Ssb(NC) or Ssb(N) formed a binary complex with Ssb(C) that displayed enhanced ssDNA binding activity. Unlike Ssb(FL), Ssb variants were able to differentially modulate topoisomerase-I activity, but failed to stimulate Deinococcal RecA-promoted DNA strand exchange. The results suggest that the C-terminal OB fold is primarily responsible for ssDNA binding. The N-terminal OB fold binds weakly to ssDNA but is involved in multimerization. (C) 2015 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies. This is an open access article under the CC BY-NC-ND license.

Ischaemic concentrations of lactate increase TREK1 channel activity by interacting with a single histidine residue in the carboxy terminal domain

Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change. AbstractA rise in lactate concentration and the leak potassium channel TREK1 have been independently associated with cerebral ischaemia. Recent literature suggests lactate to be neuroprotective and TREK1 knockout mice show an increased sensitivity to brain and spinal cord ischaemia; however, the connecting link between the two is missing. Therefore we hypothesized that lactate might interact with TREK1 channels. In the present study, we show that lactate at ischaemic concentrations (15-30mm) at pH7.4 increases TREK1 current in CA1 stratum radiatum astrocytes and causes membrane hyperpolarization. We confirm the intracellular action of lactate on TREK1 in hippocampal slices using monocarboxylate transporter blockers and at single channel level in cell-free inside-out membrane patches. The intracellular effect of lactate on TREK1 is specific since other monocarboxylates such as pyruvate and acetate at pH7.4 failed to increase TREK1 current. Deletion and point mutation experiments suggest that lactate decreases the longer close dwell time incrementally with increase in lactate concentration by interacting with the histidine residue at position 328 (H328) in the carboxy terminal domain of the TREK1 channel. The interaction of lactate with H328 is dependent on the charge on the histidine residue since isosteric mutation of H328 to glutamine did not show an increase in TREK1 channel activity with lactate. This is the first demonstration of a direct effect of lactate on ion channel activity. The action of lactate on the TREK1 channel signifies a separate neuroprotective mechanism in ischaemia since it was found to be independent of the effect of acidic pH on channel activity. Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change.

Electromagnetic analysis of novel class of multiple core/multiple clad step index single mode optical fiber by analytical means

General propagation properties and universal curves are given for double clad single mode fibers with inner cladding index higher or lower than the outer cladding index, using the parameter: inner cladding/core radii ratio. Mode cut-off conditions are also examined for the cases. It is shown that dispersion properties largely differ from the single clad single mode fiber case, leading to large new possibilities for extension of single mode operation for large wavelength tange. Paper demonstrates that how substantially we can extend the single mode operation range by using the raised inner cladding fiber. Throughout we have applied our own computations technique to find out the eigenvalue for a given modes. Detail derivations with all trivial mathematics for eigenmode equation are derived for each case. Paper also demonstrates that there is not much use of using depressed inner cladding fiber. We have also concluded that using the large inner cladding/inner core radius we can significantly increase the single mode operation range for the large wavelength region. (C) 2015 Elsevier GmbH. All rights reserved.

Growth mechanism of the interdiffusion zone between platinum modified bond coats and single crystal superalloys

Pt-modified beta-NiAl bond coats are applied over the superalloys for oxidation protection in jet engine applications. However, as shown in this study, it also enhances the growth of the interdiffusion zone developed between the bond coat and the superalloy along with brittle precipitates. Location of the Kirkendall plane indicates that a precipitate free sublayer grows from the bond coat, whereas another sublayer grows from the superalloy containing very high volume fraction of precipitates. With increasing Pt content, thickness of both the sublayers increases because of an increase in diffusion rates of the components. Quantitative electron probe microanalysis indicates high concentration of refractory components in the precipitates. Transmission electron microscopy shows that Rene N5 superalloy produces TCP phases mu and P, whereas CMSX-4 superalloy produces mu and sigma in the interdiffusion zone. With increasing Pt content in the bond coat, the average size of the precipitates decreases when coupled with Rene N5. Precipitates become much finer when the same bond coats are coupled with CMSX-4. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Gradient echo single scan inversion recovery: application to proton and fluorine relaxation studies

Single scan longitudinal relaxation measurement experiments enable rapid estimation of the spin-lattice relaxation time (T-1) as the time series of spin relaxation is encoded spatially in the sample at different slices resulting in an order of magnitude saving in time. We consider here a single scan inversion recovery pulse sequence that incorporates a gradient echo sequence. The proposed pulse sequence provides spectra with significantly enhanced signal to noise ratio leading to an accurate estimation of T-1 values. The method is applicable for measuring a range of T-1 values, thus indicating the possibility of routine use of the method for several systems. A comparative study of different single scan methods currently available is presented, and the advantage of the proposed sequence is highlighted. The possibility of the use of the method for the study of cross-correlation effects for the case of fluorine in a single shot is also demonstrated. Copyright (C) 2015 John Wiley & Sons, Ltd.

Anomalous re-entrant glassy magnetic phase in LaMn0.5Co0.5O3 single crystals

We report an anomalous re-entrant glassy magnetic phase in (l00) oriented ferromagnetic LaMn0.5Co0.5O3 single crystals. The characterization is fortified with conventional magnetometry, like linear as-well-as non-linear ac susceptibility and specific heat. As the sample is cooled below the ferromagnetic transition temperature, it reenters a glassy magnetic phase whose dynamics have little resemblance with the conventional response. The glassy transition shifts to a higher temperature with increasing frequency of the applied ac field. But it does not respond to the dc biasing or memory experiment. Specific heat as well as non-linear ac susceptibility data also do not relate to the conventional glassy response. Unusually low magnetic entropy indicates the lack of long range magnetic ordering. The results demonstrate that the glassy phase in LaMn0.5Co0.5O3 is not due to any of the known conventional origins. We infer that the competing ferromagnetic and antiferromagnetic interaction due to high B-site disorder is responsible for this anomalous re-entrant glassy phase. (C) 2016 AIP Publishing LLC.

Prussian blue as a single precursor for synthesis of Fe/Fe3C encapsulated N-doped graphitic nanostructures as bi-functional catalysts

We report a unique, single source precursor Prussian blue (iron(III) ferrocyanide (Fe-4(III)Fe-II(CN)(6)](3))) for the synthesis of Fe/Fe3C nanoparticle encapsulated N-doped graphitic layers and bamboo-like graphitic nanotubes. Hollow N-doped graphite (N-HG) nanostructures are obtained when the encapsulated nanostructures are treated with an acid. Both the encapsulated nanostructures and N-HG are shown to be applicable as bi-functional electrocatalysts for oxygen reduction (ORR) and oxygen evolution reactions (OER). The ORR activity is shown to be improved for N-HG and is comparable to commercial Pt/C. On the other hand, encapsulated nanostructures exhibit OER activity with long-term stability comparable to commercial RuO2.

Detection of quantum well induced single degenerate-transition-dipoles in ZnO nanorods

Quantifying and characterising atomic defects in nanocrystals is difficult and low-throughput using the existing methods such as high resolution transmission electron microscopy (HRTEM). In this article, using a defocused wide-field optical imaging technique, we demonstrate that a single ultrahigh-piezoelectric ZnO nanorod contains a single defect site. We model the observed dipole-emission patterns from optical imaging with a multi-dimensional dipole and find that the experimentally observed dipole pattern and model-calculated patterns are in excellent agreement. This agreement suggests the presence of vertically oriented degenerate-transition-dipoles in vertically aligned ZnO nanorods. The HRTEM of the ZnO nanorod shows the presence of a stacking fault, which generates a localised quantum well induced degenerate-transition-dipole. Finally, we elucidate that defocused wide-field imaging can be widely used to characterise defects in nanomaterials to answer many difficult questions concerning the performance of low-dimensional devices, such as in energy harvesting, advanced metal-oxide-semiconductor storage, and nanoelectromechanical and nanophotonic devices.

Growth mechanism of the interdiffusion zone between platinum modified bond coats and single crystal superalloys

Pt-modified beta-NiAl bond coats are applied over the superalloys for oxidation protection in jet engine applications. However, as shown in this study, it also enhances the growth of the interdiffusion zone developed between the bond coat and the superalloy along with brittle precipitates. Location of the Kirkendall plane indicates that a precipitate free sublayer grows from the bond coat, whereas another sublayer grows from the superalloy containing very high volume fraction of precipitates. With increasing Pt content, thickness of both the sublayers increases because of an increase in diffusion rates of the components. Quantitative electron probe microanalysis indicates high concentration of refractory components in the precipitates. Transmission electron microscopy shows that Rene N5 superalloy produces TCP phases mu and P, whereas CMSX-4 superalloy produces mu and sigma in the interdiffusion zone. With increasing Pt content in the bond coat, the average size of the precipitates decreases when coupled with Rene N5. Precipitates become much finer when the same bond coats are coupled with CMSX-4. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Gradient echo single scan inversion recovery: application to proton and fluorine relaxation studies

Single scan longitudinal relaxation measurement experiments enable rapid estimation of the spin-lattice relaxation time (T-1) as the time series of spin relaxation is encoded spatially in the sample at different slices resulting in an order of magnitude saving in time. We consider here a single scan inversion recovery pulse sequence that incorporates a gradient echo sequence. The proposed pulse sequence provides spectra with significantly enhanced signal to noise ratio leading to an accurate estimation of T-1 values. The method is applicable for measuring a range of T-1 values, thus indicating the possibility of routine use of the method for several systems. A comparative study of different single scan methods currently available is presented, and the advantage of the proposed sequence is highlighted. The possibility of the use of the method for the study of cross-correlation effects for the case of fluorine in a single shot is also demonstrated. Copyright (C) 2015 John Wiley & Sons, Ltd.

Anomalous re-entrant glassy magnetic phase in LaMn0.5Co0.5O3 single crystals

We report an anomalous re-entrant glassy magnetic phase in (l00) oriented ferromagnetic LaMn0.5Co0.5O3 single crystals. The characterization is fortified with conventional magnetometry, like linear as-well-as non-linear ac susceptibility and specific heat. As the sample is cooled below the ferromagnetic transition temperature, it reenters a glassy magnetic phase whose dynamics have little resemblance with the conventional response. The glassy transition shifts to a higher temperature with increasing frequency of the applied ac field. But it does not respond to the dc biasing or memory experiment. Specific heat as well as non-linear ac susceptibility data also do not relate to the conventional glassy response. Unusually low magnetic entropy indicates the lack of long range magnetic ordering. The results demonstrate that the glassy phase in LaMn0.5Co0.5O3 is not due to any of the known conventional origins. We infer that the competing ferromagnetic and antiferromagnetic interaction due to high B-site disorder is responsible for this anomalous re-entrant glassy phase. (C) 2016 AIP Publishing LLC.