Climate change and forests in India

Forests play a critical role in addressing climate change concerns in the broader context of global change and sustainable development. Forests are linked to climate change in three ways. i) Forests are a source of greenhouse gas (GHG) emissions: ii) Forests offer mitigation opportunities to stabilise GHG concentrations: iii) Forests are impacted by climate change. This paper reviews studies related to climate change and forests in India: first, the studies estimating carbon inventory for the Indian land use change and forestry sector (LUCF), then the different models and mitigation potential estimates for the LUCF sector in India. Finally it reviews the studies on the impact of climate change on forest ecosystems in India, identifying the implications for net primary productivity and bio-diversity. The paper highlights data, modelling and research gaps relevant to the GHG inventory, mitigation potential and vulnerability and impact assessments for the forest sector in India.

Microstructural characterization of ultrafine-grain interstitial-free steel by X-ray diffraction line profile analysis

This paper highlights the microstructural features of commercially available interstitial free (IF) steel specimens deformed by equal channel angular pressing (ECAP) up to four passes following the route A. The microstructure of the samples was studied by different techniques of X-ray diffraction peak profile analysis as a function of strain (epsilon). It was found that the crystallite size is reduced substantially already at epsilon=2.3 and it does not change significantly during further deformation. At the same time, the dislocation density increases gradually up to epsilon=4.6. The dislocation densities estimated from X-ray diffraction study are found to correlate very well with the experimentally obtained yield strength of the samples.

Intra and Inter-Molecular Communications Through Protein Structure Network

Communication within and across proteins is crucial for the biological functioning of proteins. Experiments such as mutational studies on proteins provide important information on the amino acids, which are crucial for their function. However, the protein structures are complex and it is unlikely that the entire responsibility of the function rests on only a few amino acids. A large fraction of the protein is expected to participate in its function at some level or other. Thus, it is relevant to consider the protein structures as a completely connected network and then deduce the properties, which are related to the global network features. In this direction, our laboratory has been engaged in representing the protein structure as a network of non-covalent connections and we have investigated a variety of problems in structural biology, such as the identification of functional and folding clusters, determinants of quaternary association and characterization of the network properties of protein structures. We have also addressed a few important issues related to protein dynamics, such as the process of oligomerization in multimers, mechanism on protein folding, and ligand induced communications (allosteric effect). In this review we highlight some of the investigations which we have carried out in the recent past. A review on protein structure graphs was presented earlier, in which the focus was on the graphs and graph spectral properties and their implementation in the study of protein structure graphs/networks (PSN). In this article, we briefly summarize the relevant parts of the methodology and the focus is on the advancement brought out in the understanding of protein structure-function relationships through structure networks. The investigations of structural/biological problems are divided into two parts, in which the first part deals with the analysis of PSNs based on static structures obtained from x-ray crystallography. The second part highlights the changes in the network, associated with biological functions, which are deduced from the network analysis on the structures obtained from molecular dynamics simulations.

Catalysis and mechanism of malonyl transferase activity in type II fatty acid biosynthesis acyl carrier proteins

One of the unexplored, yet important aspects of the biology of acyl carrier proteins (ACPs) is the self-acylation and malonyl transferase activities dedicated to ACPs in polyketide synthesis. Our studies demonstrate the existence of malonyl transferase activity in ACPs involved in type II fatty acid biosynthesis from Plasmodium falciparum and Escherichia coli. We also show that the catalytic malonyl transferase activity is intrinsic to an individual ACP. Mutational analysis implicates an arginine/lysine in loop II and an arginine/glutamine in helix III as the catalytic residues for transferase function. The hydrogen bonding properties of these residues appears to be indispensable for the transferase reaction. Complementation of fabD(Ts) E. coli highlights the putative physiological role of this process. Our studies thus shed light on a key aspect of ACP biology and provide insights into the mechanism involved therein.

Climate response to physiological forcing of carbon dioxide simulated by the coupled Community Atmosphere Model (CAM3.1) and Community Land Model (CLM3.0)

Increasing concentrations of atmospheric CO2 decrease stomatal conductance of plants and thus suppress canopy transpiration. The climate response to this CO2-physiological forcing is investigated using the Community Atmosphere Model version 3.1 coupled to Community Land Model version 3.0. In response to the physiological effect of doubling CO2, simulations show a decrease in canopy transpiration of 8%, a mean warming of 0.1K over the land surface, and negligible changes in the hydrological cycle. These climate responses are much smaller than what were found in previous modeling studies. This is largely a result of unrealistic partitioning of evapotranspiration in our model control simulation with a greatly underestimated contribution from canopy transpiration and overestimated contributions from canopy and soil evaporation. This study highlights the importance of a realistic simulation of the hydrological cycle, especially the individual components of evapotranspiration, in reducing the uncertainty in our estimation of climatic response to CO2-physiological forcing. Citation: Cao, L., G. Bala, K. Caldeira, R. Nemani, and G.Ban-Weiss (2009), Climate response to physiological forcing of carbon dioxide simulated by the coupled Community Atmosphere Model (CAM3.1) and Community Land Model (CLM3.0).

Allostery in tRNA Synthetases Elucidated from MD Simulations and Protein Structure Networks

tRNA synthetases (aaRS) are enzymes crucial in the translation of genetic code. The enzyme accylates the acceptor stem of tRNA by the congnate amino acid bound at the active site, when the anti-codon is recognized by the anti-codon site of aaRS. In a typical aaRS, the distance between the anti-codon region and the amino accylation site is approximately 70 Å. We have investigated this allosteric phenomenon at molecular level by MD simulations followed by the analysis of protein structure networks (PSN) of non-covalent interactions. Specifically, we have generated conformational ensembles by performing MD simulations on different liganded states of methionyl tRNA synthetase (MetRS) from Escherichia coli and tryptophenyl tRNA synthetase (TrpRS) from Human. The correlated residues during the MD simulations are identified by cross correlation maps. We have identified the amino acids connecting the correlated residues by the shortest path between the two selected members of the PSN. The frequencies of paths have been evaluated from the MD snapshots[1]. The conformational populations in different liganded states of the protein have been beautifully captured in terms of network parameters such as hubs, cliques and communities[2]. These parameters have been associated with the rigidity and plasticity of the protein conformations and can be associated with free energy landscape. A comparison of allosteric communication in MetRS and TrpRS [3] elucidated in this study highlights diverse means adopted by different enzymes to perform a similar function. The computational method described for these two enzymes can be applied to the investigation of allostery in other systems.

Beta-Ketoacyl-ACP Synthase I/II from Plasmodium falciparum (PfFabB/F)-Is it B or F?

Condensing enzymes play an important and decisive role in terms of fatty acid composition of any organism. They can be classified as condensing enzymes involved in initiating the cycle and enzymes involved in elongating the initiated fatty acyl chain. In E. coli, two isoforms for the elongation condensing enzymes (FabB and FabF) exists whereas Plasmodium genome contains only one isoform. By in vitro complementation studies in E. coli CY244 cells, we show that PfFabB/ functions like E. coli FabF as the growth of the mutant cells could rescued only in the presence of oleic acid. But unlike bacterial enzyme, PfFabB/F does not increase the cis-vaccenic acid content in the mutant cells upon lowering the growth temperature. This study thus highlights the distinct properties of P. falciparum FabF which sets it apart from E. coli and most other enzymes of this family, described so far.