A conditional random field-based downscaling method for assessment of climate change impact on multisite daily precipitation in the Mahanadi basin

Downscaling to station-scale hydrologic variables from large-scale atmospheric variables simulated by general circulation models (GCMs) is usually necessary to assess the hydrologic impact of climate change. This work presents CRF-downscaling, a new probabilistic downscaling method that represents the daily precipitation sequence as a conditional random field (CRF). The conditional distribution of the precipitation sequence at a site, given the daily atmospheric (large-scale) variable sequence, is modeled as a linear chain CRF. CRFs do not make assumptions on independence of observations, which gives them flexibility in using high-dimensional feature vectors. Maximum likelihood parameter estimation for the model is performed using limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) optimization. Maximum a posteriori estimation is used to determine the most likely precipitation sequence for a given set of atmospheric input variables using the Viterbi algorithm. Direct classification of dry/wet days as well as precipitation amount is achieved within a single modeling framework. The model is used to project the future cumulative distribution function of precipitation. Uncertainty in precipitation prediction is addressed through a modified Viterbi algorithm that predicts the n most likely sequences. The model is applied for downscaling monsoon (June-September) daily precipitation at eight sites in the Mahanadi basin in Orissa, India, using the MIROC3.2 medium-resolution GCM. The predicted distributions at all sites show an increase in the number of wet days, and also an increase in wet day precipitation amounts. A comparison of current and future predicted probability density functions for daily precipitation shows a change in shape of the density function with decreasing probability of lower precipitation and increasing probability of higher precipitation.

Response of a turbulent boundary layer to a step change in surface heat flux

Measurements of both the velocity and the temperature field have been made in the thermal layer that grows inside a turbulent boundary layer which is subjected to a small step change in surface heat flux. Upstream of the step, the wall heat flux is zero and the velocity boundary layer is nearly self-preserving. The thermal-layer measurements are discussed in the context of a self-preserving analysis for the temperature disturbance which grows underneath a thick external turbulent boundary layer. A logarithmic mean temperature profile is established downstream of the step but the budget for the mean-square temperature fluctuations shows that, in the inner region of the thermal layer, the production and dissipation of temperature fluctuations are not quite equal at the furthest downstream measurement station. The measurements for both the mean and the fluctuating temperature field indicate that the relaxation distance for the thermal layer is quite large, of the order of 1000θ0, where θ0 is the momentum thickness of the boundary layer at the step. Statistics of the thermal-layer interface and conditionally sampled measurements with respect to this interface are presented. Measurements of the temperature intermittency factor indicate that the interface is normally distributed with respect to its mean position. Near the step, the passive heat contaminant acts as an effective marker of the organized turbulence structure that has been observed in the wall region of a boundary layer. Accordingly, conditional averages of Reynolds stresses and heat fluxes measured in the heated part of the flow are considerably larger than the conventional averages when the temperature intermittency factor is small.

Conformational studies on cyclic dipeptides

An analysis of 11 crystal structures of cyclic dipeptides so far reported in the literature is made, with main reference to the internal parameters of these molecules. Preferred conformations of the side chains of cyclic dipeptides with different α-amino acid residues have been studied by classical energy calculations. The possible conformations of the DKP ring are also studied. The significance of the non-bonded interaction in deciding the pathway for conformational change has also been investigated. The agreement between theoretical results and experimental observations is quite good, both with respect to the conformation of these molecules as well as the enthalpy difference as estimated from n.m.r. studies between different conformers.

The influence of esterification of carboxyl groups of ribonuclease-a on its structure and immunological activity

The effect of modification of carboxyl groups of Ribonuclease-Aa on the enzymatic activity and the antigenic structure of the protein has been studied. Modification of four of the eleven free carboxyl groups of the protein by esterification in anhydrous methanol/0.1 M hydrochloric acid resulted in nearly 80% loss in enzymatic activity but had very little influence on the antigenic structure of the protein. Further increases in the modification of the carboxyl groups caused a progressive loss in immunological activity, and the fully methylated RNase-A exhibited nearly 30% immunological activity. Concomitant with this change in the antigenic structure of the protein, the ability of the molecule to complement with RNase-S-protein increased, clearly indicating the unfolding of the peptide "tail" from the remainder of the molecule. The susceptibility to proteolysis, accessibility of methionine residues for orthobenzoquinone reaction and the loss in immunological activity of the more extensively esterified derivatives of RNase-A are suggestive of the more flexible conformation of these derivatives as compared with the compact native conformation. The fact that even the fully methylated RNase-A retains nearly 30% of its immunological activity suggested that the modified protein contained antibody recognizable residual native structure, which presumably accommodates some antigenic determinants.

Crystal state conformation of three model monomer units for the beta-bend ribbon structure

The molecular and crystal structures of three compounds, representing the repeating units of the -bend ribbon (an approximate 310-helix, with an intramolecular hydrogen-bonding donor every two residues), have been determined by x-ray diffraction. They are Boc-Aib-Hib-NHBzl, Z-Aib-Hib-NHBzl, and Z-L-Hyp-Aib-NHMe (Aib, -aminoisobutyric acid; Bzl, benzyl; Boc, t-butyloxycarbonyl; Hyp, hydroxyproline Hib, -hydroxyisobutyric acid; Z, benzyloxycarbonyl). The two former compounds are folded in a -bend conformation: type III (III) for Boc-Aib-Hib-NHBzl, while type II (II) for the Z analogue. Conversely, the structure of Z-L-Hyp-Aib-NHMe, although not far from a type II -bend, is partially open.

X-ray studies on crystalline complexes involving amino acids and peptides. XXIII. Variability in ionization state, conformation and molecular aggregation in the complexes of succinic acid with DL- and L-lysine

Crystalline complexes of succinic acid with DL- and L-lysine have been prepared and analysed by X-ray diffraction. DL-Lysine complex: C6HIsN202 + 1 2- 1 ~C4H404 .~C4H604, Mr -- 264"2, PI, a = 5"506 (4), =8.070(2), c=14.089(2) A,, a=92.02(1), /3= 100"69 (3), y = 95"85 (3) ~>, Z = 2, Dx = 1"44 g cm -3, R = 0.059 for 2546 observed reflections. Form I of the e-lysine complex: C6HIsN20-, ~ .C4H504, Mr = 264.2, P1, a = 5" 125 (2), b = 8"087 (1), c = 8"689 (1) A,, a = 112.06 (1), /3 = 99.08 (2), y = 93"77(2) °, Z--l, D,,,=1"34(3), Dx=l"34gcm 3 R = 0.033 for 1475 observed reflections. Form II of + I 2- the e-lysine complex: C6H15N202 .,iC4H404 .- 1 I ") 4C4H604.4(C4HsO4""H'"CaH404)" , Mr = 264"2, P1, a = 10.143 (4), b = 10.256 (2), c = 12"916 (3) A,, a = 105.00 (2),/3 = 99-09 (3), y = 92"78 (3)::, Z = 4, Dm= 1"37(4), D,.= 1.38gcm 3, R=0.067 for 2809 observed reflections. The succinic acid molecules in the structures exhibit a variety of ionization states. Two of the lysine conformations found in the complexes have been observed for the first time in crystals containing lysine. Form II of the L-lysine complex is highly pseudosymmetric. In all the complexes, unlike molecules aggregate into separate alternating layers. The basic element of aggregation in the lysine layer in the complexes is an S2-type head-to-tail sequence. This element combines in different ways in the three structures. The basic element of aggre gation in the succinic acid layer in the complexes is a hydrogen-bonded ribbon. The ribbons are interconnected indirectly through amino groups in the lysine layer.

Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence.

The i + 5-->i hydrogen bonded turn conformation (pi-turn) with the fifth residue adopting alpha L conformation is frequently found at the C-terminus of helices in proteins and hence is speculated to be a "helix termination signal." An analysis of the occurrence of i + 5-->i hydrogen bonded turn conformation at any general position in proteins (not specifically at the helix C-terminus), using coordinates of 228 protein crystal structures determined by X-ray crystallography to better than 2.5 A resolution is reported in this paper. Of 486 detected pi-turn conformations, 367 have the (i + 4)th residue in alpha L conformation, generally occurring at the C-terminus of alpha-helices, consistent with previous observations. However, a significant number (111) of pi-turn conformations occur with (i + 4)th residue in alpha R conformation also, generally occurring in alpha-helices as distortions either at the terminii or at the middle, a novel finding. These two sets of pi-turn conformations are referred to by the names pi alpha L and pi alpha R-turns, respectively, depending upon whether the (i + 4)th residue adopts alpha L or alpha R conformations. Four pi-turns, named pi alpha L'-turns, were noticed to be mirror images of pi alpha L-turns, and four more pi-turns, which have the (i + 4)th residue in beta conformation and denoted as pi beta-turns, occur as a part of hairpin bend connecting twisted beta-strands. Consecutive pi-turns occur, but only with pi alpha R-turns. The preference for amino acid residues is different in pi alpha L and pi alpha R-turns. However, both show a preference for Pro after the C-termini. Hydrophilic residues are preferred at positions i + 1, i + 2, and i + 3 of pi alpha L-turns, whereas positions i and i + 5 prefer hydrophobic residues. Residue i + 4 in pi alpha L-turns is mainly Gly and less often Asn. Although pi alpha R-turns generally occur as distortions in helices, their amino acid preference is different from that of helices. Poor helix formers, such as His, Tyr, and Asn, also were found to be preferred for pi alpha R-turns, whereas good helix former Ala is not preferred. pi-Turns in peptides provide a picture of the pi-turn at atomic resolution. Only nine peptide-based pi-turns are reported so far, and all of them belong to pi alpha L-turn type with an achiral residue in position i + 4. The results are of importance for structure prediction, modeling, and de novo design of proteins.

Climate-change and agriculture - an indian perspective

In this paper, we examine the major predictions made so far regarding the nature of climate change and its impacts on our region in the light of the known errors of the set of models and the observations over this century. The major predictions of the climate models about the impact of increased concentration of greenhouse gases ave at variance with the observations over the Indian region during the last century characterized by such increases and global warming. It is important to note that as far as the Indian region is concerned, the impact of year-to-year variation of the monsoon will continue to be dominant over longer period changes even in the presence of global warming. Recent studies have also brought out the uncertainties in the yields simulated by crop models. It is suggested that a deeper understanding of the links between climate and agricultural productivity is essential for generating reliable predictions of impact of climate change. Such an insight is also required for identifying cropping patterns and management practices which are tailored for sustained maximum yield in the face of the vagaries of the monsoon.

Antibodies specific for 1-methylguanosine as a probe of tRNA conformation

Antibodies specific for 1-methylguanosine (m1G) were produced by immunization of rabbits with a bovine serum albumin conjugate of m1G. Antibodies specificity was determined by measuring the inhibition of binding of 3H-m1G trialcohol by various nucleosides or related derivatives. The relative affinities of the unpurified antibodies for various nucleosides showed that m1G trialcohol had an 8-fold higher affinity than m1G; further, guanosine and 2'-O-methylguanosine had at least a 500-fold lower affinity than m1G. The antibodies were purified on m1G-AH-Sepharose column and subsequently immobilized to Sepharose. Immobilized m1G antibodies quantitatively and exclusively retained m1G-containing oligonucleotides derived from ribonuclease A digests of 32P-labeled phage T4 tRNAPro. On the other hand, intact 32P-labeled T4 tRNAPro or its precursor RNA(s) did not bind to the same column. These findings indicate that at least a portion of m1G adjacent to the 3' end of the anticodon in intact T4 tRNAPro is not accessible for antibody binding.

The 310 helical conformation of a pentapeptide containing a-aminoisobutyric acid (Aib): X-ray crystal structure of Tos-(Aib)5 OMe

The pentapeptide Tos-(Aib)5-OMe adopts a 310 helical conformation in the solid state, with three consecutive Type III B-turns stabilized by intramolecular hydrogen bonds.

X-Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl-(Aib-Pro)4methyl ester. Evidence for a novel helical structure

The synthesis of the octapeptide, benzyloxycarbonyl-(-aminoisobutyryl-L-prolyl)4-methyl ester [Z-(Aib-Pro)4-OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen-deuterium exchange. 13C studies are consistent with a structure involving only trans Aib-Pro bonds, while ir experiments support a hydrogen-bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III -turns with Aib and Pro at the corners and stabilized by 4 1 intramolecular hydrogen bonds.

Type II beta-turn conformation of pivaloyl-L-prolyl-a-aminoiso-butyryl-N-methylamide: Theoretical, spectroscopic and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamihdaes been shown to possess one intramolecular hydrogen bond in (CD&SO solution, by 'H-nmr methods, suggesting the existence of p-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II P-turn conformations are about 2 kcal mol-' more stable than Type 111 structures. A crystallographic study has established the Type I1 /%turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 8, b = 11.421 A, c = 12.966 A, /3 = 97.55", and 2 = 2. The structure has been refined to a final R value of 0.061. The Type I1 p-turn conformation is stabilized by an intramolecular 4 - 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are @pro= -57.8", $pro = 139.3', @Aib = 61.4', and $Ajb = 25.1'. The Type 11 /%turn conformation for Pro-Aib in this peptide is compared with the Type I11 structures observed for the same segment in larger peptides.

Carbon sequestration versus bioenergy: A case study from South India exploring the relative land-use efficiency of two options for climate change mitigation

This case study has been carried out as a comparison between two different land-use strategies for climate change mitigation, with possible application within the Clean Development Mechanisms. The benefits of afforestation for carbon sequestration versus for bioenergy production are compared in the context of development planning to meet increasing domestic and agricultural demand for electricity in Hosahalli village, Karnataka, India. One option is to increase the local biomass based electricity generation, requiring an increased biomass plantation area. This option is compared with fossil based electricity generation where the area is instead used for producing wood for non-energy purposes while also sequestering carbon in the soil and standing biomass. The different options have been assessed using the PRO-COMAP model. The ranking of the different options varies depending on the system boundaries and time period. Results indicate that, in the short term (30 years) perspective, the mitigation potential of the long rotation plantation is largest, followed by the short rotation plantation delivering wood for energy. The bioenergy option is however preferred if a long-term view is taken. Short rotation forests delivering wood for short-lived non-energy products have the smallest mitigation potential, unless a large share of the wood products are used for energy purposes (replacing fossil fuels) after having served their initial purpose. If managed in a sustainable manner all of these strategies can contribute to the improvement of the social and environmental situation of the local community. (C) 2009 Elsevier Ltd. All rights reserved.

Melting of an Anchored Bilayer: Phase Transitions in the Organic-Inorganic Hybrid Pervoskite (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n=11, 13, 15, 17)

The conformation, organization, and phase transitions of alkyl chains in organic-inorganic hybrids based on the double pervoskite-slab lead iodides, (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n = 11, 13, 15, 17) have been investigated by X-ray diffraction, calorimetry, and infrared vibrational spectroscopy. In these hybrid solids, double pervoskite (CH3NH3)Pb2I7 slabs are interleaved with alkyl ammonium chains with the anchored alkyl chains arranged as tilted bilayers and adopting a planar all-trans conformation at room temperature. The (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 compounds exhibit a single reversible phase transition above room temperature with the associated enthalpy change varying linearly with alkyl chain length. This transition corresponds to the melting in two-dimensions of the alkyl chains of the anchored bilayer and is characterized by increased conformational disorder of the methylene units of the chain and loss of tilt angle coherence leading to an increase in the interslab spacing. By monitoring features in the infrared spectra that are characteristic of the global conformation of the alkyl chains, a quantitative relation between conformational disorder and melting of the anchored bilayer is established. It is found that, irrespective of the alkyl chain length, melting occurs when at least 60% of the chains in the anchored bilayer of (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 have one or more gauche defects. This concentration is determined by the underlying lattice to which the alkyl chains are anchored.