Indian Ocean sea surface salinity variations in a coupled model

The variability of the sea surface salinity (SSS) in the Indian Ocean is studied using a 100-year control simulation of the Community Climate System Model (CCSM 2.0). The monsoon-driven seasonal SSS pattern in the Indian Ocean, marked by low salinity in the east and high salinity in the west, is captured by the model. The model overestimates runoff int the Bay of Bengal due to higher rainfall over the Himalayan-Tibetan regions which drain into the Bay of Bengal through Ganga-Brahmaputra rivers. The outflow of low-salinity water from the Bay of Bengal is to strong in the model. Consequently, the model Indian Ocean SSS is about 1 less than that seen in the climatology. The seasonal Indian Ocean salt balance obtained from the model is consistent with the analysis from climatological data sets. During summer, the large freshwater input into the Bay of Bengal and its redistribution decide the spatial pattern of salinity tendency. During winter, horizontal advection is the dominant contributor to the tendency term. The interannual variability of the SSS in the Indian Ocean is about five times larger than that in coupled model simulations of the North Atlantic Ocean. Regions of large interannual standard deviations are located near river mouths in the Bay of Bengal and in the eastern equatorial Indian Ocean. Both freshwater input into the ocean and advection of this anomalous flux are responsible for the generation of these anomalies. The model simulates 20 significant Indian Ocean Dipole (IOD) events and during IOD years large salinity anomalies appear in the equatorial Indian Ocean. The anomalies exist as two zonal bands: negative salinity anomalies to the north of the equator and positive to the south. The SSS anomalies for the years in which IOD is not present and for ENSO years are much weaker than during IOD years. Significant interannual SSS anomalies appear in the Indian Ocean only during IOD years.

The determination of spatial pattern in Dictyostelium discoideum

Free-living amoebae of the cellular slime mould Dictyostelium discoideum aggregate when starved and give rise to a long and thin multicellular structure, the slug. The slug resembles a metazoan embryo, and as with other embryos it is possible to specify a fate map. In the case of Dictyostelium discoideum the map is especially simple: cells in the anterior fifth of the slug die and form a stalk while the majority of those in the posterior differentiate into spores. The genesis of this anterior-posterior distinction is the subject of our review. In particular, we ask: what are the relative roles of individual pre-aggregative predispositions and post-aggregative position in determining cell fate? We review the literature on the subject and conclude that both factors are important. Variations in nutritional status, or in cell cycle phase at starvation, can bias the probability that an amoeba differentiates into a stalk cell or a spore. On the other hand, isolates, or slug fragments, consisting of only prestalk cells or only prespore cells can regulate so as to result in a normal range of both cell types. We identify three levels of control, each being responsible for guiding patterning in normal development: (i) 'coin tossing', whereby a cell autonomously exhibits a preference for developing along either the stalk or the spore pathway with relative probabilities that can be influenced by the environment; (ii) 'chemical kinetics', whereby prestalk and prespore cells originate from undifferentiated amoebae on a probabilistic basis but, having originated, interact (e.g. via positive and negative feedbacks), and the interaction influences the possibility of conversion of one cell type into the other, and (iii) 'positional information', in which the spatial distribution of morphogens in the slug influences the pathway of differentiation. In the case of possibilities (i) and (ii), sorting out of like cell types leads to the final spatial pattern. In the case of possibility (iii), the pattern arises in situ.

Spatial variations of effective elastic thickness over the Ninetyeast Ridge and implications for its structure and tectonic evolution

We present new data on the strength of oceanic lithosphere along the Ninetyeast Ridge (NER) from two independent methods: spectral analysis (Bouguer coherence) using the fan wavelet transform technique, and spatial analysis (flexure inversion) with the convolution method. The two methods provide effective elastic thickness (T-e) patterns that broadly complement each other, and correlate well with known surface structures and regional-scale features. Furthermore, our study presents a new high resolution database on the Moho configuration, which obeys flexural isostasy, and exhibit regional correlations with the T-e variations. A continuous ridge structure with a much lower T-e value than that of normal oceanic lithosphere provides strong support for the hotspot theory. The derived T-e values vary over the northern (higher T-e similar to 10-20 km), central (anomalously low T-e similar to 0-5 km), and southern (low T-e similar to 5 km) segments of the NER. The lack of correlation of the T-e value with the progressive aging of the lithosphere implies differences in thermo-mechanical setting of the crust and underlying mantle in different parts of the NER, again indicating diversity in their evolution. The anomalously low T-e and deeper Moho (similar to 22 km) estimates of the central NER (between 0.5 degrees N and 17 degrees S) are attributed to the interaction of a hotspot with the Wharton spreading ridge that caused significant thermal rejuvenation and hence weakening of the lithosphere. The higher mechanical strength values in the northern NER (north of 0.5 degrees N) may support the idea of off-ridge emplacement and a relatively large plate motion at the time of volcanism. The low T-e and deeper Moho (similar to 22 km) estimates in the southern part (south of 17 degrees S) suggest that the lithosphere was weak and therefore younger at the time of volcanism, and this supports the idea that the southern NER was emplaced on the edge of the Indian plate. (C) 2013 Elsevier B.V. All rights reserved.

Non-linear regression model for spatial variation in precipitation chemistry for South India

Chemical composition of rainwater changes from sea to inland under the influence of several major factors - topographic location of area, its distance from sea, annual rainfall. A model is developed here to quantify the variation in precipitation chemistry under the influence of inland distance and rainfall amount. Various sites in India categorized as 'urban', 'suburban' and 'rural' have been considered for model development. pH, HCO3, NO3 and Mg do not change much from coast to inland while, SO4 and Ca change is subjected to local emissions. Cl and Na originate solely from sea salinity and are the chemistry parameters in the model. Non-linear multiple regressions performed for the various categories revealed that both rainfall amount and precipitation chemistry obeyed a power law reduction with distance from sea. Cl and Na decrease rapidly for the first 100 km distance from sea, then decrease marginally for the next 100 km, and later stabilize. Regression parameters estimated for different cases were found to be consistent (R-2 similar to 0.8). Variation in one of the parameters accounted for urbanization. Model was validated using data points from the southern peninsular region of the country. Estimates are found to be within 99.9% confidence interval. Finally, this relationship between the three parameters - rainfall amount, coastline distance, and concentration (in terms of Cl and Na) was validated with experiments conducted in a small experimental watershed in the south-west India. Chemistry estimated using the model was in good correlation with observed values with a relative error of similar to 5%. Monthly variation in the chemistry is predicted from a downscaling model and then compared with the observed data. Hence, the model developed for rain chemistry is useful in estimating the concentrations at different spatio-temporal scales and is especially applicable for south-west region of India. (C) 2008 Elsevier Ltd. All rights reserved.

Variations in the levels of aminoacylation and modified nucleotide content between total tRNAs from chloroplasts and etioplasts in cucumber cotyledons

Total tRNAs isolated from chloroplasts and etioplasts of cucumber cotyledons were compared with respect toamino 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 tRNAmodifying 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.

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.

Experimental study of the damping coefficient variations in zinc crystal

Much work has been done on obtaining empirical stress-velocity relations and evaluating the temperature dependence and activation energy of plastic deformation /1, 2/. Another prevalent concept is that of the drag coefficient and its variation with degree of crystal imperfection /3/. Significant differences and discrepancies exist in the reported values /2, 4/. Although it is recognised that the yield point is caused by point interstitials and aggregates, little has been done on the evaluation of specific crystal-solute combinations and interaction parameters. Some of the first efforts, in this direction were performed by Wain and Cottrell /5/.

The scale-invariance of spatial patterning in a developing system

Regulating systems, that is, those which exhibit scale-invariant patterns in the adult, are supposed, to do so on account of interactions between cells during development. The nature of these interactions has to be such that the system of positional information (ldquomaprdquo) in the embryo also regulates. To our knowledge, this supposition regarding a regulating map has not been subjected to a direct test in any embryonic system. Here we do so by means of a simple and novel criterion and use it to examine tip regeneration in the mulicellular stage (slug) ofDictyostelium discoideum. When anterior, tip-containing fragments of slugs are amputated, a new tip spontaneously regenerates at the cut surface of the (remaining) posterior fragment. The time needed for regeneration to occur depends on the relative size of the amputated fragment but is independent of the total size of the slug. We conclude from this finding that there is at least one system underlying positional information in the slug which regulates.

Mesospheric temperature response to variations in geomagnetic activity

Temperature data collected over several years from rocket grenade and other experiments at Point Barrow (Alaska), Fort Churchill (Canada) and Wallops Island (Virginia) have been analysed to determine the effect of geomagnetic activity on the neutral temperature in the mesosphere and to study the latitudinal variation of this effect. An analysis carried out has revealed almost certainly significant correlations between the temperature and the geomagnetic indicies Kp and Ap at Fort Churchill and marginally significant correlations at Barrow and Wallops. This has also been substantiated by a linear regression analysis. The results indicate two types of interdependence between mesospheric temperature and geomagnetic field variations. The first type is the direct heating effect, during a geomagnetic disturbance, which has been observed in the present analysis with a time lag of 3–15 hr at the high latitudes and 36 hr at the middle latitudes. The magnitude of this heating effect has been found to decrease at the lower altitudes. The second type of interrelation which has been observed is temperature perturbations preceding geomagnetic field variations, both presumably caused by a disturbance in atmospheric circulation at these levels.

Spatial correlation in grain misorientation distribution

Grain misorientation was studied in relation to the nearest neighbor's mutual distance using electron back-scattered diffraction measurements. The misorientation correlation function was defined as the probability density for the occurrence of a certain misorientation between pairs of grains separated by a certain distance. Scale-invariant spatial correlation between neighbor grains was manifested by a power law dependence of the preferred misorientation vs. inter-granular distance in various materials after diverse strain paths. The obtained negative scaling exponents were in the range of -2 +/- 0.3 for high-angle grain boundaries. The exponent decreased in the presence of low-angle grain boundaries or dynamic recrystallization, indicating faster decay of correlations. The correlations vanished in annealed materials. The results were interpreted in terms of lattice incompatibility and continuity conditions at the interface between neighboring grains. Grain-size effects on texture development, as well as the implications of such spatial correlations on texture modeling, were discussed.

Variations in the Levels of Chloroplast tRNAs and Aminoacyl-tRNA Synthetases in Senescing Leaves of Phaseolus vulgaris

The relative amounts of chloroplast tRNAs(Leu), tRNA(Glu), tRNA(Phe), tRNAs(Thr), and tRNA(Tyr) and of chloroplastic and cytoplasmic aminoacyl-tRNA synthetases were compared in green leaves, yellowing senescing leaves, and N(6)-benzyladenine-treated senescing leaves from bean (Phaseolus vulgaris, var Contender). Aminoacylation of the tRNAs using Escherichia coli aminoacyl-tRNA synthetases indicated that in senescing leaves the relative amount of chloroplast tRNA(Phe) was significantly lower than in green leaves. Senescing leaves treated with N(6)-benzyladenine contained higher levels of this tRNA than untreated senescing leaves. No significant change in the relative amounts of chloroplast tRNAs(Leu), tRNAs(Thr), and tRNA(Tyr) was detected in green, yellow senescing, or N(6)-benzyladine-treated senescing leaves. Relative levels of chloroplast tRNAs were also estimated by hybridization of tRNAs to DNA blots of gene specific probes. These experiments confirmed the results obtained by aminoacylation and revealed in addition that the relative level of chloroplast tRNA(Glu) is higher in senescing leaves than in green leaves. Transcription run-on assays indicated that these changes in tRNA levels are likely to be due to a differential rate of degradation rather than to a differential rate of transcription of the tRNA genes. Chloroplastic and cytoplasmic leucyl-, phenylalanyl-, and tyrosyl-tRNA synthetase activities were greatly reduced in senescing leaves as compared to green leaves, whereas N(6)-benzyladenine-treated senescing leaves contained higher enzyme activities than untreated senescing leaves. These results suggest that during senescence, as well as during senescence-retardation by cytokinins, changes in enzyme activities, such as aminoacyl-tRNA synthetases, rather than reduced levels of tRNAs, affect the translational capacity of chloroplasts.

OFDM-MAC algorithms and their impact on TCP performance in next generation mobile networks

Next generation wireless systems employ Orthogonal frequency division multiplexing (OFDM) physical layer owing to the high data rate transmissions that are possible without increase in bandwidth. While TCP performance has been extensively studied for interaction with link layer ARQ, little attention has been given to the interaction of TCP with MAC layer. In this work, we explore cross-layer interactions in an OFDM based wireless system, specifically focusing on channel-aware resource allocation strategies at the MAC layer and its impact on TCP congestion control. Both efficiency and fairness oriented MAC resource allocation strategies were designed for evaluating the performance of TCP. The former schemes try to exploit the channel diversity to maximize the system throughput, while the latter schemes try to provide a fair resource allocation over sufficiently long time duration. From a TCP goodput standpoint, we show that the class of MAC algorithms that incorporate a fairness metric and consider the backlog outperform the channel diversity exploiting schemes.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structuralvariations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structural variations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.