Insights into conformational and packing features in a series of aryl substituted ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate

The supramolecular structures of eight aryl protected ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine- 5-carboxylates have been analyzed to determine the role of different functional groups on the molecular geometry, conformational characteristics and the packing of these molecules in the crystal lattice. Out of these the para fluoro substituted compound on the aryl ring exhibits conformational polymorphism, due to the different conformation of the ester moiety. This behaviour has been characterized using both powder and single-crystal X-ray diffraction, optical microscopy and differential scanning calorimetry performed on both these polymorphs. The compounds pack via the cooperative interplay of strong N-H center dot center dot center dot O=C intermolecular dimers and chains forming a sheet like structure. In addition, weak C-H center dot center dot center dot O=C and C-H center dot center dot center dot pi interactions impart additional stability to the crystal packing.

Polarization Changes of Radiation through Stimulated Raman Scattering

We study change in the polarization of electromagnetic waves due to the stimulated Raman scattering in a plasma. In this process an electromagnetic wave undergoes coherent scattering off an electron plasma wave. It is found that some of the observed polarization properties such as the rapid temporal variations, sense reversal, rotation of the plane of polarization, and change of nature of polarization in the case of pulsars and quasars could be accounted for through stimulated Raman scattering.

Understanding changes in the Himalayan cryosphere using remote sensing techniques

In the Himalayas, a large area is covered by glaciers and seasonal snow and changes in its extent can influence availability of water in the Himalayan Rivers. In this paper, changes in glacial extent, glacial mass balance and seasonal snow cover are discussed. Glacial retreat was estimated for 1868 glaciers in 11 basins distributed in the Indian Himalaya since 1962. The investigation has shown an overall reduction in glacier area from 6332 to 5329km2 from 1962 to 2001/2 - an overall deglaciation of 16%. Snow line at the end of ablation season on the Chhota Shigri glacier observed using field and satellite methods suggests a change in altitude from 4900 to 5200m from the late 1970s to present. Seasonal snow cover was monitored in the 28 river sub-basins using normalized difference snow index (NDSI) technique in Central and Western Himalaya. The investigation has shown that in the early part of winter, i.e. from October to December, a large amount of snow retreat was observed. For many basins located in lower altitude and in the south of the Pir Panjal range, snow ablation was observed throughout the winter season. In addition, average stream runoff of the Baspa basin for the month of December increased by 75%. This combination of glacial retreat, negative mass balance, early melting of seasonal snow cover and winter-time increase in stream runoff might suggest an influence of global warming on the Himalayan cryosphere.

5-Fluorouracil induces structural changes in rat liver tRNA

5-fluorouracil (FUra) has been shown to modulate the aminoacylation function of rat liver tRNA. The present study was aimed at studying the structure-function relationship of FUra-substituted tRNA. Male Wistar rats (2-3 month old) were given a single i.p. injection of FUra at 50, 250, or 500 mg/kg body wt. and FUra-substituted total liver tRNA, i.e. tRNA(FUra50, 250, and 500, respectively, were isolated 3 h later. Normal tRNA (tRNA(N)) was isolated from saline-treated control rats. Thermal denaturation studies showed higher melting temperatures for tRNA(FUra) compared to tRNA(N). Heat denaturation followed by renaturation of total tRNA did not affect the activity of tRNA(N) and tRNA(FUra50), where as tRNA(FUra250 and 500) lost 35% and 72% of activity, respectively, compared to the corresponding group of non-denatured tRNA. Antibodies specific to rat liver tRNA recognized normal and FUra-substituted tRNA in the order of tRNA(N) > tRNA(FUra50) > or = tRNA(FUra250) > tRNA(FUra500) in an avidin-biotin micro-enzyme linked immunosorbant assay. tRNA(N) or tRNA(FUra50) preincubated with tRNA antiserum showed 74% and 59% of aminoacylation activity, respectively, compared to that of corresponding tRNA preincubated with normal rabbit IgG. However, activities of similarly treated tRNA(FUra250 and 500) were not affected. The observations of possible changes in the secondary structure of rat liver tRNA upon incorporation of FUra are discussed.

Correlation of seasonal changes in sperm output with endocrinological changes in the adult male bonnet monkey, Macaca radiata

We have examined the monthly variations in sperm output and attempted to correlate the profiles of endocrine hormones secreted with the sperm counts throughout the ,year in the adult male bonnet monkey. As previously reported, there was a distinct spurt in sperm output beginning September through December months. A concomitant increase in serum testosterone and prolactin concentrations were also noted during September through November (mid and post-monsoon season). Although there was a marked increase in gonadotropin releasing hormone stimulated testosterone secretion, the peak testosterone concentrations post gonadotropin releasing hormone injection did not vary significantly (P>0.05) throughout the year. Basal serum follicle stimulating hormone concentrations did not vary significantly (P>0.05) during April to June months compared to September-November months. Serum inhibin concentration remained unaltered throughout the year, except in the month of March. The results of this study provide evidence for annual rhythms in prolactin and testosterone secretion and a distinct seasonality in the sperm output of the adult male bonnet monkey, but the pituitary responsiveness to exogenous gonadotropin releasing hormone remains unaltered throughout the year. Because of the existence of seasonality as noted in the present study, future studies which utilize the adult male bonnet monkey as an experimental model need to take into consideration the seasonal effects on reproductive function in this species.

Effect of mutations on the p53 IRES RNA structure Implications for de-regulation of the synthesis of p53 isoforms

Earlier we have demonstrated the presence of internal ribosome entry site (IRES) within tumor suppressor p53 mRNA. Here we have mapped the putative secondary structure of p53-IRES RNA using information from chemical probing and nuclease mapping experiments. Additionally, the secondary structure of the IRES element of the wild-type RNA was compared with cancer-derived silent mutant p53 RNAs. These mutations might result in the conformational alterations of p53-IRES RNAs. The results also indicate decreased IRES activities of the mutants as compared to wild-type RNA. Further, it was observed that some of the cytoplasmic trans-acting factors, critical for enhancing IRES function, were unable to bind mutant RNAs as efficiently as to wild-type. Our results suggest that hnRNP C1/C2 binds to p53-IRES and siRNA mediated partial silencing of hnRNP C1/C2 showed appreciable decrease in IRES function and consequent decrease in the level of the corresponding p53 isoform. Interestingly mutant p53 IRES showed lesser binding with hnRNP C1/C2 protein. Finally, upon doxorubicin treatment, the mutant RNAs were unable to show enhanced p53 synthesis to similar extent compared to wild type. Taken together, these observations suggest that mutations occurring in the p53 IRES might have profound implications for de-regulation of its expression and activity.

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Probing Single and Bilayer Graphene Field Effect Transistors By Raman Spectroscopy

This article is a review of our work related to Raman studies of single layer and bilayer graphenes as a function Fermi level shift achieved by electrochemically top gating a field effect transistor. Combining the transport and in situ Raman studies of the field effect devices, a quantitative understanding is obtained of the phonon renormalization due to doping of graphene. Results are discussed in the light of time dependent perturbation theory, with electron phonon coupling parameter as an input from the density functional theory. It is seen that phonons near and Gamma and K points of the Brillouin zone are renormalized very differently by doping. Further, Gamma-phonon renormalization is different in bilayer graphene as compared to single layer, originating from their different electronic band structures near the zone boundary K-point. Thus Raman spectroscopy is not only a powerful probe to characterize the number of layers and their quality in a graphene sample, but also to quantitatively evaluate electron phonon coupling required to understand the performance of graphene devices.

Probing the inter-tube transport in aligned and random multiwall carbon nanotubes

The temperature and magnetic field dependence of conductivity has been used to probe the inter-tube transport in multiwall carbon nanotubes (MWNTs). The scanning electron microscopy images show highly aligned and random distribution of MWNTs. The conductivity in aligned carbon nanotube (ACNT) and random carbon nanotube (RCNT) samples at low temperature follows T-1/2 (at T < 8 K) and T-3/4 (at T > 8 K) dependence in accordance with the weak localization and electron-electron (e-e) interaction model. The values of diffusion coefficient in ACNT and RCNT are 0.25 x 10(-2) and 0.71 x 10(-2) cm(2) s(-1), respectively, indicating that larger number of inter-tube junctions in later enhances the bulk transport. The positive magnetoconductance (MC) data in both samples show that the weak localization contribution is dominant. However, the saturation of MC at higher fields and lower temperatures indicate that e-e interaction is quite significant in RCNT. The T-3/4 and T-1/2 dependence of inelastic scattering length (l(in)) in ACNT and RCNT samples show that the inelastic e-e scattering is more important in aligned tubes. (C) 2011 American Institute of Physics. doi:10.1063/1.3552911]

Probing potential energy surfaces in confined systems: behavior of mean-square displacement in zeolites

Time evolution of mean-squared displacement based on molecular dynamics for a variety of adsorbate-zeolite systems is reported. Transition from ballistic to diffusive behavior is observed for all the systems. The transition times are found to be system dependent and show different types of dependence on temperature. Model calculations on a one-dimensional system are carried out which show that the characteristic length and transition times are dependent on the distance between the barriers, their heights, and temperature. In light of these findings, it is shown that it is possible to obtain valuable information about the average potential energy surface sampled under specific external conditions.

Cardiac remodeling in Drosophila arises from changes in actin gene expression and from a contribution of lymph gland-like cells to the heart musculature

Understanding the basis of normal heart remodeling can provide insight into the plasticity of the cardiac state, and into the potential for treating diseased tissue. In Drosophila, the adult heart arises during metamorphosis from a series of events, that include the remodeling of an existing cardiac tube, the elaboration of new inflow tracts, and the addition of a layer of longitudinal muscle fibers. We have identified genes active in all these three processes, and studied their expression in order to characterize in greater detail normal cardiac remodeling. Using a Transglutaminase-lacZ transgenic line, that is expressed in the inflow tracts of the larval and adult heart, we confirm the existence of five inflow tracts in the adult structure. In addition, expression of the Actin87E actin gene is initiated in the remodeling cardiac tube, but not in the longitudinal fibers, and we have identified an Act87E promoter fragment that recapitulates this switch in expression. We also establish that the longitudinal fibers are multinucleated, characterizing these cells as specialized skeletal muscles. Furthermore, we have defined the origin of the longitudinal fibers, as a subset of lymph gland cells associated with the larval dorsal vessel. These studies underline the myriad contributors to the formation of the adult Drosophila heart, and provide new molecular insights into the development of this complex organ. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Time-resolved fluorescence studies on covalently linked porphyrin�nitroarene complexes. Conformational control of photoinduced electron transfer reactions

Time-resolved fluorescence studies were carried out on a series of free-base and zinc(II) derivatives of meso-tetraphenylporphyrins covalently linked to either 1,3-dinitrobenzene (DNB) or 1,3,5-trinitrobenzene (TNB) acceptor units. These acceptor units were linked at different sites (at the ortho, meta or para positions of one of the phenyl groups of meso-tetraphenylporphyrin) to the donor porphyrins such that the resulting isomeric intramolecular donor-acceptor complexes exhibit different centre-to-centre (ctc) distances and relative orientations. Biexponential fluorescence decay profiles observed for several of these covalently linked complexes were rationalized in terms of the presence of ''closed'' and ''extended'' conformers. Detailed analyses of the fluorescence decay data have provided a comprehensive understanding of the photoinduced electron transfer (PET) reactions occurring in systems containing zinc(II) porphyrin donors. It is observed that although DNB-linked zinc(II) complexes follow the trends predicted for the efficiency of PET with respect to donor-acceptor distance, the TNB-linked zinc(II) porphyrins exhibit a behaviour which is dictated by steric effects. Similarly, although the thermodynamic criteria predict a greater efficiency of charge separation in TNB-linked complexes compared with DNB-linked complexes, the reverse trend observed has been attributed to orientational effects. In the complexes containing free-base porphyrin donors, PET is expected to be less efficient from a thermodynamic viewpoint. In a few of these cases, fluorescence quenching seems to occur by parallel mechanisms other than PET.

Lipid conformational nomenclature: a general method

We propose a conformational nomenclature for amphiphilic lipid molecules that is general and compatible with the stereospecific numbering scheme, in contrast to earlier methods in which discrepancies with the sn-scheme lead to contradictory assignments of the absolute configuration of the system. The present method can be rationally extended to different classes of lipids, both natural and synthetic. It is simple and provides a convenient framework for conformational studies on widely varying classes of lipids.

Conformational preferences of α-functionalised keten-S,N-acetals: Potential role of SO and SS interactions in solution

PMR spectra of carbonyl compounds 2a-k reveal significant variations in the population of E and Z isomers on changing the solvent from CDCl3 to DMSO-d6. In non-polar media, the intramolecular N-H…. O hydrogen bonded form is exclusively observed. In DMSO-d6, the alternative Z form is also populated. A similar conformational switch is also noted in the corresponding thiones. Different interpretations are critically analysed. The most consistent explanation is suggested to involvean interplay of N-H….X hydrogen bonding and S…X attractive interaction (X = O,S) in these systems. Ab initio calculations support this interpretation.