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.

Micro-satellite angular rate estimation using second-order sliding mode observer

Development of computationally efficient and accurate attitude rate estimation algorithm using low-cost commercially available star sensor arrays and processing unit for micro-satellite mission is presented. Our design reduces the computational load of least square (LS)-based rate estimation method while maintaining the same accuracy compared to other rate estimation approaches. Furthermore, rate estimation accuracy is improved by using recently developed fast and accurate second-order sliding mode observer (SOSMO) scheme. It also gives robust estimation in the presence of modeling uncertainties, unknown disturbances, and measurement noise. Simulation study shows that rate estimation accuracy achieved by our LS-based method is comparable with other methods for a typical commercially available star sensor array. The robustness analysis of SOSMO with respect to measurement noise is also presented in this paper. Simulation test bench for a practical scenario of satellite rate estimation uses moment-of-inertia variation and environmental disturbances affecting a typical micro-satellite at 500km circular orbit. Comparison studies of SOSMO with 1-SMO and pseudo-linear Kalman filter show that satisfactory estimation accuracy is achieved by SOSMO.

A Facile Synthesis of 1,5-Disubstituted Tetrazole Peptidomimetics by Desulfurization/Electrocyclization of Thiopeptides

The cis-amide bond isostere, 1,5-disubstituted tetrazole,has been introduced in the peptide backbone by a simple route starting from the thiopeptide. The desired 1,5-disubstituted tetrazole peptidomimetics were synthesized by the desulfurization of thiopeptides by using HgCl2 in the presence of NaN3/TEA in DMF in good yields. Various other thiophilic reagents including hypervalent iodine reagents failed to deliver the tetrazole product with the exception of CBr4/PPh3, which resulted in moderate yields. The advantage of the present protocol over previous methods has been demonstrated by the selective insertion of tetrazole into peptide-thiopeptide hybrids. Also, the protocol is compatible with commonly employed urethane protecting groups (Fmoc, Boc, and Cbz) in peptide chemistry. Thiopeptide Boc-Pro-CSNH]-Val-OMe (2i) and two tetrazole peptidomimetics Cbz-Ala-CN4]-Phe-OMe (3d) and Boc-Pro-CN4]-Val-OMe (3i) were obtained as single crystals and their molecular structures have been confirmed by X-ray crystallography.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Pressure-induced phase transition in Bi2Se3 at 3 GPa: electronic topological transition or not?

In recent years, a low pressure transition around P similar to 3 GPa exhibited by the A(2)B(3)-type 3D topological insulators is attributed to an electronic topological transition (ETT) for which there is no direct evidence either from theory or experiments. We address this phase transition and other transitions at higher pressure in bismuth selenide (Bi2Se3) using Raman spectroscopy at pressure up to 26.2 GPa. We see clear Raman signatures of an isostructural phase transition at P similar to 2.4 GPa followed by structural transitions at similar to 10 GPa and 16 GPa. First-principles calculations reveal anomalously sharp changes in the structural parameters like the internal angle of the rhombohedral unit cell with a minimum in the c/a ratio near P similar to 3 GPa. While our calculations reveal the associated anomalies in vibrational frequencies and electronic bandgap, the calculated Z(2) invariant and Dirac conical surface electronic structure remain unchanged, showing that there is no change in the electronic topology at the lowest pressure transition.

Population Recovery of Nicobar Long-Tailed Macaque Macaca fascicularis umbrosus following a Tsunami in the Nicobar Islands, India

Natural disasters pose a threat to isolated populations of species with restricted distributions, especially those inhabiting islands. The Nicobar long tailed macaque. Macaca fascicularis umbrosus, is one such species found in the three southernmost islands (viz. Great Nicobar, Little Nicobar and Katchal) of the Andaman and Nicobar archipelago, India. These islands were hit by a massive tsunami (Indian Ocean tsunami, 26 December 2004) after a 9.2 magnitude earthquake. Earlier studies Umapathy et al. 2003; Sivakumar, 2004] reported a sharp decline in the population of M. f. umbrosus after thetsunami. We studied the distribution and population status of M. f. umbrosus on thethree Nicobar Islands and compared our results with those of the previous studies. We carried out trail surveys on existing paths and trails on three islands to get encounter rate as measure of abundance. We also checked the degree of inundation due to tsunami by using Normalized Difference Water Index (NDWI) on landsat imageries of the study area before and after tsunami. Theencounter rate of groups per kilometre of M. f. umbrosus in Great Nicobar, Little Nicobar and Katchal was 0.30, 0.35 and 0.48 respectively with the mean group size of 39 in Great Nicobar and 43 in Katchal following the tsunami. This was higher than that reported in the two earlier studies conducted before and after the tsunami. Post tsunami, there was a significant change in the proportion of adult males, adult females and immatures, but mean group size did not differ as compared to pre tsunami. The results show that population has recovered from a drastic decline caused by tsunami, but it cannot be ascertained whether it has reached stability because of the altered group structure. This study demonstrates the effect of natural disasters on island occurring species.

Electrical and Plasmonic Properties of Ligand-Free Sn4+-Doped In2O3 (ITO) Nanocrystals

Sn4+-doped In2O3 (ITO) is a benchmark transparent conducting oxide material. We prepared ligand-free but colloidal ITO (8nm, 10% Sn4+) nanocrystals (NCs) by using a post-synthesis surface-modification reaction. (CH3)(3)OBF4 removes the native oleylamine ligand from NC surfaces to give ligand-free, positively charged NCs that form a colloidal dispersion in polar solvents. Both oleylamine-capped and ligand-free ITO NCs exhibit intense absorption peaks, due to localized surface plasmon resonance (LSPR) at around =1950nm. Compared with oleylamine-capped NCs, the electrical resistivity of ligand-free ITO NCs is lower by an order of magnitude (approximate to 35mcm(-1)). Resistivity over a wide range of temperatures can be consistently described as a composite of metallic ITO grains embedded in an insulating matrix by using a simple equivalent circuit, which provides an insight into the conduction mechanism in these systems.

Cold gas in cluster cores: global stability analysis and non-linear simulations of thermal instability

We perform global linear stability analysis and idealized numerical simulations in global thermal balance to understand the condensation of cold gas from hot/virial atmospheres (coronae), in particular the intracluster medium (ICM). We pay particular attention to geometry (e.g. spherical versus plane-parallel) and the nature of the gravitational potential. Global linear analysis gives a similar value for the fastest growing thermal instability modes in spherical and Cartesian geometries. Simulations and observations suggest that cooling in haloes critically depends on the ratio of the cooling time to the free-fall time (t(cool)/t(ff)). Extended cold gas condenses out of the ICM only if this ratio is smaller than a threshold value close to 10. Previous works highlighted the difference between the nature of cold gas condensation in spherical and plane-parallel atmospheres; namely, cold gas condensation appeared easier in spherical atmospheres. This apparent difference due to geometry arises because the previous plane-parallel simulations focused on in situ condensation of multiphase gas but spherical simulations studied condensation anywhere in the box. Unlike previous claims, our non-linear simulations show that there are only minor differences in cold gas condensation, either in situ or anywhere, for different geometries. The amount of cold gas depends on the shape of tcool/tff; gas has more time to condense if gravitational acceleration decreases towards the centre. In our idealized plane-parallel simulations with heating balancing cooling in each layer, there can be significant mass/energy/momentum transfer across layers that can trigger condensation and drive tcool/tff far beyond the critical value close to 10.