NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

An estimate of equilibrium sensitivity of global terrestrial carbon cycle using NCAR CCSM4

Increasing concentrations of atmospheric CO2 influence climate, terrestrial biosphere productivity and ecosystem carbon storage through its radiative, physiological and fertilization effects. In this paper, we quantify these effects for a doubling of CO2 using a low resolution configuration of the coupled model NCAR CCSM4. In contrast to previous coupled climate-carbon modeling studies, we focus on the near-equilibrium response of the terrestrial carbon cycle. For a doubling of CO2, the radiative effect on the physical climate system causes global mean surface air temperature to increase by 2.14 K, whereas the physiological and fertilization on the land biosphere effects cause a warming of 0.22 K, suggesting that these later effects increase global warming by about 10 % as found in many recent studies. The CO2-fertilization leads to total ecosystem carbon gain of 371 Gt-C (28 %) while the radiative effect causes a loss of 131 Gt-C (10 %) indicating that climate warming damps the fertilization-induced carbon uptake over land. Our model-based estimate for the maximum potential terrestrial carbon uptake resulting from a doubling of atmospheric CO2 concentration (285-570 ppm) is only 242 Gt-C. This highlights the limited storage capacity of the terrestrial carbon reservoir. We also find that the terrestrial carbon storage sensitivity to changes in CO2 and temperature have been estimated to be lower in previous transient simulations because of lags in the climate-carbon system. Our model simulations indicate that the time scale of terrestrial carbon cycle response is greater than 500 years for CO2-fertilization and about 200 years for temperature perturbations. We also find that dynamic changes in vegetation amplify the terrestrial carbon storage sensitivity relative to a static vegetation case: because of changes in tree cover, changes in total ecosystem carbon for CO2-direct and climate effects are amplified by 88 and 72 %, respectively, in simulations with dynamic vegetation when compared to static vegetation simulations.

The effect of minor addition of Ni on the microstructural evolution and mechanical properties of suction cast Al-0.14 at. pct Sc binary alloy

Aluminum scandium binary alloys represent a promising precipitation-hardening alloy system. However, the hardness of the binary alloys decreases with the rapid coarsening of Al3Sc precipitate during high-temperature aging. In the current study, we report a new approach to compensate for the loss of mechanical properties by combining rapid solidification with very small ternary addition of transition metal Ni. This addition yields dispersion, and at a critical concentration improves the mechanical properties. We explore additions of a maximum of 0.06 at. pct of Nickel to a binary Al-0.14 at. pct Sc alloy, which yield nickel-rich dispersions. We report two kinds of biphasic dispersions containing AlNi2Sc/Al9Ni2 and alpha-Al/Al9Ni2 phase combinations. The maximum improvement in mechanical properties occurs with the addition of 0.045 at. pct Ni with a yield strength of 239 +/- A 7 MPa for an aging treatment at 583 K (310 A degrees C) for 15 hours. DOI: 10.1007/s11661-013-1624-z (C) The Minerals, Metals & Materials Society and ASM International 2013

An experimental set-up for carbon isotopic analysis of atmospheric CO2 and an example of ecosystem response during solar eclipse 2010

We present here, an experimental set-up developed for the first time in India for the determination of mixing ratio and carbon isotopic ratio of air-CO2. The set-up includes traps for collection and extraction of CO2 from air samples using cryogenic procedures, followed by the measurement of CO2 mixing ratio using an MKS Baratron gauge and analysis of isotopic ratios using the dual inlet peripheral of a high sensitivity isotope ratio mass spectrometer (IRMS) MAT 253. The internal reproducibility (precision) for the PC measurement is established based on repeat analyses of CO2 +/- 0.03 parts per thousand. The set-up is calibrated with international carbonate and air-CO2 standards. An in-house air-CO2 mixture, `OASIS AIRMIX' is prepared mixing CO2 from a high purity cylinder with O-2 and N-2 and an aliquot of this mixture is routinely analyzed together with the air samples. The external reproducibility for the measurement of the CO2 mixing ratio and carbon isotopic ratios are +/- 7 (n = 169) mu mol.mol(-1) and +/- 0.05 (n = 169) parts per thousand based on the mean of the difference between two aliquots of reference air mixture analyzed during daily operation carried out during November 2009-December 2011. The correction due to the isobaric interference of N2O on air-CO2 samples is determined separately by analyzing mixture of CO2 (of known isotopic composition) and N2O in varying proportions. A +0.2 parts per thousand correction in the delta C-13 value for a N2O concentration of 329 ppb is determined. As an application, we present results from an experiment conducted during solar eclipse of 2010. The isotopic ratio in CO2 and the carbon dioxide mixing ratio in the air samples collected during the event are different from neighbouring samples, suggesting the role of atmospheric inversion in trapping the emitted CO2 from the urban atmosphere during the eclipse.

Unprecedented formation of a 14-membered dihydropyran macrocycle via sequential olefin cross metathesis-intramolecular hetero Diels-Alder reaction

Formation of a 2,3-dihydro-4H-pyran containing 14-membered macrocycle by sequential olefin cross metathesis and a highly regiospecific hetero Diels-Alder reaction was observed in the reaction of a hydroxydienone derived from tartaric acid with Grubbs' second generation catalyst. It was found that the free alcohol in the hydroxyenone led to the macrocycle formation, while protection of the hydroxy group formed the ring closing metathesis product. (C) 2013 Elsevier Ltd. All rights reserved.

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

On the epochal variation of intensity of tropical cyclones in the Arabian Sea

During recent years, an increase in the intensity of pre-monsoon tropical cyclones (TCs) is observed over the Arabian Sea. This study suggests that this increase is due to epochal variability in the intensity of TCs and is associated with epochal variability in the storm-ambient vertical wind shear and tropical cyclone heat potential (TCHP). There is a significant increase (0.53kJcm(-2)year(-1)) of TCHP during recent years. The warmer upper ocean helps TCs to sustain or increase their intensity by an uninterrupted supply of sensible and latent heat fluxes from the ocean surface to the atmosphere.

Stable atmospheric methane in the 2000s: key-role of emissions from natural wetlands

Two atmospheric inversions (one fine-resolved and one process-discriminating) and a process-based model for land surface exchanges are brought together to analyse the variations of methane emissions from 1990 to 2009. A focus is put on the role of natural wetlands and on the years 2000-2006, a period of stable atmospheric concentrations. From 1990 to 2000, the top-down and bottom-up visions agree on the time-phasing of global total and wetland emission anomalies. The process-discriminating inversion indicates that wetlands dominate the time-variability of methane emissions (90% of the total variability). The contribution of tropical wetlands to the anomalies is found to be large, especially during the post-Pinatubo years (global negative anomalies with minima between -41 and -19 Tg yr(-1) in 1992) and during the alternate 1997-1998 El-Nino/1998-1999 La-Nina (maximal anomalies in tropical regions between +16 and +22 Tg yr(-1) for the inversions and anomalies due to tropical wetlands between +12 and +17 Tg yr(-1) for the process-based model). Between 2000 and 2006, during the stagnation of methane concentrations in the atmosphere, the top-down and bottom-up approaches agree on the fact that South America is the main region contributing to anomalies in natural wetland emissions, but they disagree on the sign and magnitude of the flux trend in the Amazon basin. A negative trend (-3.9 +/- 1.3 Tg yr(-1)) is inferred by the process-discriminating inversion whereas a positive trend (+1.3 +/- 0.3 Tg yr(-1)) is found by the process model. Although processed-based models have their own caveats and may not take into account all processes, the positive trend found by the B-U approach is considered more likely because it is a robust feature of the process-based model, consistent with analysed precipitations and the satellite-derived extent of inundated areas. On the contrary, the surface-data based inversions lack constraints for South America. This result suggests the need for a re-interpretation of the large increase found in anthropogenic methane inventories after 2000.

Specific Sequence of a Beta Turn in Human La Protein May Contribute to Species Specificity of Hepatitis C Virus

Human La protein is known to be an essential host factor for translation and replication of hepatitis C virus (HCV) RNA. Previously, we have demonstrated that residues responsible for interaction of human La protein with the HCV internal ribosomal entry site (IRES) around the initiator AUG within stem-loop IV form a beta-turn in the RNA recognition motif (RRM) structure. In this study, sequence alignment and mutagenesis suggest that the HCV RNA-interacting beta-turn is conserved only in humans and chimpanzees, the species primarily known to be infected by HCV. A 7-mer peptide corresponding to the HCV RNA-interacting region of human La inhibits HCV translation, whereas another peptide corresponding to the mouse La sequence was unable to do so. Furthermore, IRES-mediated translation was found to be significantly high in the presence of recombinant human La protein in vitro in rabbit reticulocyte lysate. We observed enhanced replication with HCV subgenomic and full-length replicons upon overexpression of either human La protein or a chimeric mouse La protein harboring a human La beta-turn sequence in mouse cells. Taken together, our results raise the possibility of creating an immunocompetent HCV mouse model using human-specific cell entry factors and a humanized form of La protein.

Mono- and Dialkyne Insertion Reactions of Cyclopalladated N,N `,N `'-Triarylguanidines kappa(2)(C,N)Pd(mu-Br)](2) and cis-/trans-kappa(2)(C,N)Pd(Lewis Base)Br]. Scaffolds for Enlarged, Rearranged, and Zwitterionic Palladacycles through Ring Contraction cum Amine-Imine Tautomerization

Insertion reactions of six-membered cyclopalladated N,N',N''-triarylguanidines, kappa(2)(C,N)Pd(mu-Br)](2) with various alkynes in CH2Cl2 under ambient conditions afforded diinserted eight-membered palladacycles, (kappa(2)(C,N):eta(2)(C=C)-PdBr] (1-11), in high yield (76-96%), while insertion reactions of six-membered cyclopalladated N,N',N''-triarylguanidines, kappa(2)(C,N)Pd(Lewis base)Br] (VI-XI), with various alkynes under the aforementioned conditions afforded monoinserted six-membered palladacycles, kappa(2)(C,N)-Pd(Lewis base)Br] (12-21), in high yield (81-91%) except for 14 (23%). The insertion reaction of VI with 2 equiv of dimethyl acetylenedicarboxylate (DMAD) and the insertion reaction of 12 with 1 equiv of DMAD in CH2Cl2 under ambient conditions resulted in the formation of a diinserted zwitterionic five-membered palladacycle, kappa(2)(C,C)Pd(2,6-lutidine)Br] (22), in 76% and 70% yields, respectively. Palladacycle 22 upon reaction with AgOTf in wet MeCN afforded the ionic palladacycle kappa(2)(C,C)Pd(2,6-lutidine)(H2O)]OTf] (23) in 78% yield. The ring size of the ``kappa(2)(C,N)Pd]'' unit in the structurally characterized diinserted palladacycles (1 center dot 2CH(2)Cl(2)center dot H2O, 2, 5, and 7), and monoinserted palladacycles (17, 18, and 20 center dot C7H8 H2O) is smaller than that anticipated for mono- and diinserted palladacycles, and this feature is mainly ascribed to the proclivity of III-XI to undergo ring contraction cum amine-imine tautomerization upon alkyne insertion. Palladacycle 22 represents the first diinserted product obtained in alkyne insertion reactions of kappa(2)(C,N)Pd(Lewis base)X] type palladarycles. The molecular structure of 22 center dot H2O determined by X-ray diffraction indicates that the positive charge on the guanidinium moiety is balanced by the negative charge on the palladium atom and thus represents the first structurally characterized zwitterionic palladacycle to be reported in alkyne insertion chemistry. Plausible mechanisms of formation of 12-21 and 22 have been outlined. The presence of more than one species in solution for some of the palladacycles in the series 1-7 and 12-21 was explained by invoking the C-N single-bond rotation of the CN3 unit of the guanidine moiety, while this process in conjunction with Pd-N(lutidine) bond rotation was invoked to explain the presence of four isomers of 15, as studied with the aid of variable-concentration H-1 NMR experiments carried out for 14 and 15.

Performance analysis of FSO links under strong atmospheric turbulence conditions using various modulation schemes

Strong atmospheric turbulence is a major hindrance in wireless optical communication systems. In this paper, the performance of a wireless optical communication system is analyzed using different modulation formats such as, binary phase shift keying-subcarrier intensity modulation (BPSK-SIM), differential phase shift keying (DPSK), differential phase shift keying-subcarrier intensity modulation (DPSK-SIM), Mary pulse position modulation (M-PPM) and polarization shift keying (PoISK). The atmospheric channel is modeled for strong atmospheric turbulences with combined effect of turbulence and pointing errors. Novel closed-form analytical expressions for average bit error rate (BER), channel capacity and outage probability for the various modulation techniques, viz. BPSK-SIM, DPSK, DPSK-SIM, PoISK and M-PPM are derived. The simulated results for BER, channel capacity and outage probability of various modulation techniques are plotted and analyzed. (C) 2014 Elsevier GmbH. All rights reserved.

Development and Evaluation of Statistical Downscaling Models for Monthly Precipitation

Several statistical downscaling models have been developed in the past couple of decades to assess the hydrologic impacts of climate change by projecting the station-scale hydrological variables from large-scale atmospheric variables simulated by general circulation models (GCMs). This paper presents and compares different statistical downscaling models that use multiple linear regression (MLR), positive coefficient regression (PCR), stepwise regression (SR), and support vector machine (SVM) techniques for estimating monthly rainfall amounts in the state of Florida. Mean sea level pressure, air temperature, geopotential height, specific humidity, U wind, and V wind are used as the explanatory variables/predictors in the downscaling models. Data for these variables are obtained from the National Centers for Environmental Prediction-National Center for Atmospheric Research (NCEP-NCAR) reanalysis dataset and the Canadian Centre for Climate Modelling and Analysis (CCCma) Coupled Global Climate Model, version 3 (CGCM3) GCM simulations. The principal component analysis (PCA) and fuzzy c-means clustering method (FCM) are used as part of downscaling model to reduce the dimensionality of the dataset and identify the clusters in the data, respectively. Evaluation of the performances of the models using different error and statistical measures indicates that the SVM-based model performed better than all the other models in reproducing most monthly rainfall statistics at 18 sites. Output from the third-generation CGCM3 GCM for the A1B scenario was used for future projections. For the projection period 2001-10, MLR was used to relate variables at the GCM and NCEP grid scales. Use of MLR in linking the predictor variables at the GCM and NCEP grid scales yielded better reproduction of monthly rainfall statistics at most of the stations (12 out of 18) compared to those by spatial interpolation technique used in earlier studies.

An insight to the low temperature conduction mechanism of c-axis grown Al-doped ZnO, a widely used transparent conducting oxide

Al-doped ZnO thin films were synthesized from oxygen reactive co-sputtering of Al and Zn targets. Explicit doping of Al in the highly c-axis oriented crystalline films of ZnO was manifested in terms of structural optical and electrical properties. Electrical conduction with different extent of Al doping into the crystal lattice of ZnO (AZnO) were characterized by frequency dependent (40 Hz-50 MHz) resistance. From the frequency dependent resistance, the ac conduction of them, and correlations of localized charge particles in the crystalline films were studied. The dc conduction at the low frequency region was found to increase from 8.623 mu A to 1.14 mA for the samples AZnO1 (1 wt% Al) and AZnO2 (2 wt% Al), respectively. For the sample AZnO10 (10 wt% Al) low frequency dc conduction was not found due to the electrode polarization effect. The measure of the correlation length by inverse of threshold frequency (omega(0)) showed that on application of a dc electric field such length decreases and the decrease in correlation parameter(s) indicates that the correlation between potentials wells of charge particles decreases for the unidirectional nature of dc bias. The comparison between the correlation length and the extent of correlation in the doped ZnO could not be made due to the observation of several threshold frequencies at the extent of higher doping. Such threshold frequencies were explained by the population possibility of correlated charge carriers that responded at different frequencies. For AZnO2 (2% Al), the temperature dependent (from 4.5 to 288 K) resistance study showed that the variable range hopping mechanism was the most dominating conduction mechanism at higher temperature whereas at low temperature region it was influenced by the small polaronic hopping conduction mechanism. There was no significant influence found in these mechanisms on applications of 1, 2 and 3 V as biases.

Diurnal and seasonal variation of mixing ratio and delta C-13 of air CO2 observed at an urban station Bangalore, India

We present here observations on diurnal and seasonal variation of mixing ratio and delta C-13 of air CO2, from an urban station-Bangalore (BLR), India, monitored between October 2008 and December 2011. On a diurnal scale, higher mixing ratio with depleted delta C-13 of air CO2 was found for the samples collected during early morning compared to the samples collected during late afternoon. On a seasonal scale, mixing ratio was found to be higher for dry summer months (April-May) and lower for southwest monsoon months (June-July). The maximum enrichment in delta C-13 of air CO2 (-8.04 +/- 0.02aEuro degrees) was seen in October, then delta C-13 started depleting and maximum depletion (-9.31 +/- 0.07aEuro degrees) was observed during dry summer months. Immediately after that an increasing trend in delta C-13 was monitored coincidental with the advancement of southwest monsoon months and maximum enrichment was seen again in October. Although a similar pattern in seasonal variation was observed for the three consecutive years, the dry summer months of 2011 captured distinctly lower amplitude in both the mixing ratio and delta C-13 of air CO2 compared to the dry summer months of 2009 and 2010. This was explained with reduced biomass burning and increased productivity associated with prominent La Nina condition. While compared with the observations from the nearest coastal and open ocean stations-Cabo de Rama (CRI) and Seychelles (SEY), BLR being located within an urban region captured higher amplitude of seasonal variation. The average delta C-13 value of the end member source CO2 was identified based on both diurnal and seasonal scale variation. The delta C-13 value of source CO2 (-24.9 +/- 3aEuro degrees) determined based on diurnal variation was found to differ drastically from the source value (-14.6 +/- 0.7aEuro degrees) identified based on seasonal scale variation. The source CO2 identified based on diurnal variation incorporated both early morning and late afternoon sample; whereas, the source CO2 identified based on seasonal variation included only afternoon samples. Thus, it is evident from the study that sampling timing is one of the important factors while characterizing the composition of end member source CO2 for a particular station. The difference in delta C-13 value of source CO2 obtained based on both diurnal and seasonal variation might be due to possible contribution from cement industry along with fossil fuel / biomass burning as predominant sources for the station along with differential meteorological conditions prevailed.

Probable maximum precipitation estimation for catchments in Mahanadi river basin

Probable maximum precipitation (PMP) is a theoretical concept that is widely used by hydrologists to arrive at estimates for probable maximum flood (PMF) that find use in planning, design and risk assessment of high-hazard hydrological structures such as flood control dams upstream of populated areas. The PMP represents the greatest depth of precipitation for a given duration that is meteorologically possible for a watershed or an area at a particular time of year, with no allowance made for long-term climatic trends. Various methods are in use for estimation of PMP over a target location corresponding to different durations. Moisture maximization method and Hershfield method are two widely used methods. The former method maximizes the observed storms assuming that the atmospheric moisture would rise up to a very high value estimated based on the maximum daily dew point temperature. On the other hand, the latter method is a statistical method based on a general frequency equation given by Chow. The present study provides one-day PMP estimates and PMP maps for Mahanadi river basin based on the aforementioned methods. There is a need for such estimates and maps, as the river basin is prone to frequent floods. Utility of the constructed PMP maps in computing PMP for various catchments in the river basin is demonstrated. The PMP estimates can eventually be used to arrive at PMF estimates for those catchments. (C) 2015 The Authors. Published by Elsevier B.V.