Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

Impact of moisture variations on the circulation of the south-west monsoon

The impact of moisture anomalies on the circulation of the south-west Indian monsoon has been studied with a general circulation model. Newtonian relaxation is adopted to subject the model atmosphere under sustained moisture anomalies. The impact of negative anomalies of moisture was seen as a divergent circulation anomaly, while the positive anomaly was a stronger convergent anomaly. Although the humidity fields display a resilient behaviour, and relax back to normal patterns 1–2 days after the forcing terms in humidity are withdrawn, the circulation anomalies created by the moisture variation keeps growing. A feedback between positive moisture anomalies and low level convergence exists, which is terminated in the absence of external forcings.

Interannual variations of Indian summer monsoon in a GCM: External conditions versus internal feedbacks

The potential predictability of the Indian summer monsoon due to slowly varying sea surface temperature (SST) forcing is examined. Factors responsible for limiting the predictability are also investigated. Three multiyear simulations with the R30 version of the Geophysical Fluid Dynamics Laboratory's climate model are carried out for this purpose, The mean monsoon simulated by this model is realistic including the mean summer precipitation over the Indian continent. The interannual variability of the large-scale component of the monsoon such as the "monsoon shear index" and its teleconnection with Pacific SST is well simulated by the model in a 15-yr integration with observed SST as boundary condition. On regional scales, the skill in simulating the interannual variability of precipitation over the Indian continent by the model is rather modest and its simultaneous correlation with eastern Pacific SST is negative but poor as observed. The poor predictability of precipitation over the Indian region in the model is related to the fact that contribution to the interannual variability over this region due to slow SST variations [El Nino-Southern Oscillation (ENSO) related] is comparable to those due to regional-scale fluctuations unrelated to ENSO SST. The physical mechanism through which ENSO SST tend to produce reduction in precipitation over the Indian continent is also elucidated. A measure of internal variability of the model summer monsoon is obtained from a 20-yr integration of the same model with fixed annual cycle SST as boundary conditions but with predicted soil moisture and snow cover. A comparison of summer monsoon indexes between this run and the observed SST run shows that the internal oscillations can account for a large fraction of the simulated monsoon variability. The regional-scale oscillations in the observed SST run seems to arise from these internal oscillations. It is discovered that most of the interannual internal variability is due to an internal quasi-biennial oscillation (QBO) of the model atmosphere. Such a QBO is also found in the author's third 18-yr simulation in which fixed annual cycle of SST as well as soil moisture and snow cover are prescribed. This shows that the model QBO is not due to land-surface-atmosphere interaction. It is proposed that the model QBO arises due to an interaction between nonlinear intraseasonal oscillations and the annual cycle. Spatial structure of the QBO and its role in limiting the predictability of the Indian summer monsoon is discussed.

Variations in the Levels of Aminoacylation and Modified Nucleotide Content Between Total Transfer-RNAS From Chloroplasts and Etioplasts in Cucumber Cotyledons

Total tRNAs isolated from chloroplasts and etioplasts of cucumber cotyledons were compared with respect to amino acid acceptance, isoacceptor distribution and extent of modification. Aminoacylation of the tRNAs with nine different amino acids studied indicated that the relative acceptor activities of chloroplast total tRNAs for four amino acids are significantly higher than etioplast total tRNAs. Two dimensional polyacrylamide gel electrophoresis (2D-PAGE) of chloroplast total tRNAs separated at least 32 spots, while approximately 41 spots were resolved from etioplast total tRNAs. Comparison of the reversed-phase chromatography (RPC-5) profiles of chloroplast and etioplast leucyl-, lysyl-, phenylalanyl-, and valyl-tRNA species showed no qualitative differences in the elution profiles. However, leucyl-, lysyl- and valyl-tRNA species showed quantitative differences in the relative amounts of the isoaccepting species present in chloroplasts and etioplasts. The analysis of modified nucleotides of total tRNAs from the two plastid types indicated that total tRNA from etioplasts was undermodified with respect to ribothymidine, isopentenyladenosine/hydroxy-isopentenyladenosine, 1-methylguanosine and 2-o-methylguanosine. This indicates that illumination may cause de novo synthesis of chloroplast tRNA-modifying enzymes encoded for by nuclear genes leading to the formation of highly modified tRNAs in chloroplasts. Based on these results, we speculate that the observed decrease in levels of aminoacylation, variations in the relative amounts of certain isoacceptors, and differences in the electrophoretic mobilities of some extra tRNA spots in the etioplast total tRNAs as compared to chloroplast total tRNAs could be due to some partially undermodified etioplast tRNAs. Taken together, the data suggested that the light-induced transformation of etioplasts into chloroplasts is accompanied by increases in the relative levels of some functional chloroplast tRNAs by post transcriptional nucleotide modifications.

Studies on the variations in compression strengths of graphite powders bearing glass-epoxy composites exposed to humid conditions

The moisture absorption and changes in compression strengths in glass-epoxy (G-E composites without and with discrete quantities of graphite powders introduced into the resin mix prior to its spreading on specific glass fabric (layers) during the lay-up (stacking) sequence forms the subject matter of this report. The results point to higher moisture absorption for graphite bearing specimens. The strengths of graphite-free coupons show a continuous decrease, while the filler bearing ones show an initial rise followed by a drop for larger exposure times. Scanning Fractographic features were examined for an understanding of the process. The observations were explained invoking the effect of matrix plasticizing and the role of interfacial regions.

The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations

Background: Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles. Results: Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains. Conclusions: Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.

Nonlinear Dynamics of Beams with Stochastic Parameter Variations

The aim of this paper is to investigate the steady state response of beams under the action of random support motions. The study is of relevance in the context of earthquake response of extended land based structures such as pipelines and long span bridges, and, secondary systems such as piping networks in nuclear power plant installations. The following complicating features are accounted for in the response analysis: (a) differential support motions: this is characterized in terms of cross power spectral density functions associated with distinct support motions, (b) nonlinear support conditions, and (c) stochastically inhomogeneous stiffness and mass variations of the beam structure; questions on non-Gaussian models for these variations are considered. The method of stochastic finite elements is combined with equivalent linearization technique and Monte Carlo simulations to obtain response moments.

Inverse models to analyze the spatiotemporal variations of chemical weathering fluxes in a granito-gneissic watershed: Mule Hole, South India

Water-rock reactions are driven by the influx of water, which are out of equilibrium with the mineral assemblage in the rock. Here a mass balance approach is adopted to quantify these reactions. Based on field experiments carried out in a granito-gneissic small experimental watershed (SEW), Mule Hole SEW (similar to 4.5 km(2)), quartz, oligoclase, sericite, epidote and chlorite are identified as the basic primary minerals while kaolinite, goethite and smectite are identified as the secondary minerals. Observed groundwater chemistry is used to determine the weathering rates, in terms of `Mass Transfer Coefficients' (MTCs), of both primary and secondary minerals. Weathering rates for primary and secondary minerals are quantified in two steps. In the first step, top red soil is analyzed considering precipitation chemistry as initial phase and water chemistry of seepage flow as final phase. In the second step, minerals present in the saprolite layer are analyzed considering groundwater chemistry as the output phase. Weathering rates thus obtained are converted into weathering fluxes (Q(weathering)) using the recharge quantity. Spatial variability in the mineralogy observed among the thirteen wells of Mule Hole SEW is observed to be reflected in the MTC results and thus in the weathering fluxes. Weathering rates of the minerals in this silicate system varied from few 10 mu mol/L (in case of biotite) to 1000 s of micromoles per liter (calcite). Similarly, fluxes of biotite are observed to be least (7 +/- 5 mol/ha/yr) while those of calcite are highest (1265 791 mol/ha/yr). Further, the fluxes determined annually for all the minerals are observed to be within the bandwidth of the standard deviation of these fluxes. Variations in these annual fluxes are indicating the variations in the precipitation. Hence, the standard deviation indicated the temporal variations in the fluxes, which might be due to the variations in the annual rainfall. Thus, the methodology adopted defines an inverse way of determining weathering fluxes, which mainly contribute to the groundwater concentration. (C) 2011 Elsevier B.V. All rights reserved.

Modeling of the Effects of Process Variations on Circuit Delay at 65nm

A novel methodology for modeling the effects of process variations on circuit delay performance is proposed by relating the variations in process parameters to variations in delay metric of a complex digital circuit. The delay of a 2-input NAND gate with 65nm gate length transistors is extensively characterized by mixed-mode simulations which is then used as a library element. The variation in saturation current Ionat the device level, and the variation in rising/falling edge stage delay for the NAND gate at the circuit level, are taken as performance metrics. A 4-bit x 4-bit Wallace tree multiplier circuit is used as a representative combinational circuit to demonstrate the proposed methodology. The variation in the multiplier delay is characterized, to obtain delay distributions, by an extensive Monte Carlo analysis. An analytical model based on CV/I metric is proposed, to extend this methodology for a generic technology library with a variety of library elements.