An interdisciplinary framework to evaluate bioshield plantations: Insights from peninsular India

Bioshields or coastal vegetation structures are currently amongst the most important coastal habitat modification activities in south-east Asia, particularly after the December 2004 tsunami. Coastal plantations have been promoted at a large scale as protection against severe natural disasters despite considerable debate over their efficacy as protection measures. In this paper, we provide an interdisciplinary framework for evaluating and monitoring coastal plantations. We then use this framework in a case study in peninsular India. We conducted a socio-ecological questionnaire-based survey on government and non-government organizations directly involved in coastal plantation efforts in three 2004 Indian Ocean tsunami affected states in mainland India. We found that though coastal protection was stated to be the primary cause, socio-economic factors like providing rural employment were strong drivers of plantation activities. Local communities were engaged primarily as daily wage labour for plantation. rather than in the planning or monitoring phases. Application of ecological criteria has been undermined during the establishment and maintenance of plantations and there was a general lack of awareness about conservation laws relating to coastal forests. While ample flow of international aid has fuelled the plantation of exotics in the study area particularly after the Indian Ocean tsunami in 2004, the long term ecological consequences need further evaluation and rigorous monitoring in the future. (C) 2014 Elsevier Masson SAS. All rights reserved.

Importance of non-conserved distal carboxyl terminal amino acids in two peptidases belonging to the M1 family: Thermoplasma acidophilum Tricorn interacting factor F2 and Escherichia coli Peptidase N

Enzymes belonging to the M1 family play important cellular roles and the key amino acids (aa) in the catalytic domain are conserved. However, C-terminal domain aa are highly variable and demonstrate distinct differences in organization. To address a functional role for the C-terminal domain, progressive deletions were generated in Tricorn interacting factor F2 from Thermoplasma acidophilum (F2) and Peptidase N from Escherichia coli (PepN). Catalytic activity was partially reduced in PepN lacking 4 C-terminal residues (PepNΔC4) whereas it was greatly reduced in F2 lacking 10 C-terminal residues (F2ΔC10) or PepN lacking eleven C-terminal residues (PepNΔC11). Notably, expression of PepNΔC4, but not PepNΔC11, in E. coliΔpepN increased its ability to resist nutritional and high temperature stress, demonstrating physiological significance. Purified C-terminal deleted proteins demonstrated greater sensitivity to trypsin and bound stronger to 8-amino 1-napthalene sulphonic acid (ANS), revealing greater numbers of surface exposed hydrophobic aa. Also, F2 or PepN containing large aa deletions in the C-termini, but not smaller deletions, were present in high amounts in the insoluble fraction of cell extracts probably due to reduced protein solubility. Modeling studies, using the crystal structure of E. coli PepN, demonstrated increase in hydrophobic surface area and change in accessibility of several aa from buried to exposed upon deletion of C-terminal aa. Together, these studies revealed that non-conserved distal C-terminal aa repress the surface exposure of apolar aa, enhance protein solubility, and catalytic activity in two soluble and distinct members of the M1 family.

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Self-organization of multiple components in a steroidal hydrogel matrix: design, construction and studies on novel tunable luminescent gels and xerogels

The present work combines two rapidly growing research areas-functional supramolecular gels and lanthanide based hybrid materials. Facile hydrogel formation from several lanthanide(III) cholates has been demonstrated. The morphological and mechanical properties of these cholate gels were investigated by TEM and rheology. The hydrogel matrix was subsequently utilized for the sensitization of Tb(III) by doping a non-coordinating chromophore, 2,3-dihydroxynaphthalene (DHN), at micromolar concentrations. In the mixed gels of Tb(III)-Eu(III), an energy transfer pathway was found to operate from Tb(III) to Eu(III) and by utilizing this energy transfer, tunable multiple-color luminescent hydrogels were obtained. The emissive properties of the hydrogels were also retained in the xerogels and their suspensions in n-hexane were used for making luminescent coating on glass surface.

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

The evolution of complexity in social organization-A model using dominance-subordinate behavior in two social wasp species

Dominance and subordinate behaviors are important ingredients in the social organizations of group living animals. Behavioral observations on the two eusocial species Ropalidia marginata and Ropalidia cyathiformis suggest varying complexities in their social systems. The queen of R. cyathiformis is an aggressive individual who usually holds the top position in the dominance hierarchy although she does not necessarily show the maximum number of acts of dominance, while the R. marginata queen rarely shows aggression and usually does not hold the top position in the dominance hierarchy of her colony. In R. marginata, more workers are involved in dominance-subordinate interactions as compared to R. cyathiformis. These differences are reflected in the distribution of dominance-subordinate interactions among the hierarchically ranked individuals in both the species. The percentage of dominance interactions decreases gradually with hierarchical ranks in R. marginata while in R. cyathiformis it first increases and then decreases. We use an agent-based model to investigate the underlying mechanism that could give rise to the observed patterns for both the species. The model assumes, besides some non-interacting individuals, the interaction probabilities of the agents depend on their pre-differentiated winning abilities. Our simulations show that if the queen takes up a strategy of being involved in a moderate number of dominance interactions, one could get the pattern similar to R. cyathiformis, while taking up the strategy of very low interactions by the queen could lead to the pattern of R. marginata. We infer that both the species follow a common interaction pattern, while the differences in their social organization are due to the slight changes in queen as well as worker strategies. These changes in strategies are expected to accompany the evolution of more complex societies from simpler ones.

Organization dependent collective magnetic properties of secondary nanostructures with differential spatial ordering and magnetic easy axis orientation

Achieving control on the formation of different organization states of magnetic nanoparticles is crucial to harness their organization dependent physical properties in desired ways. In this study, three organization states of iron oxide nanoparticles (gamma-Fe2O3), defining as (i) assembly (ii) network aggregate and (iii) cluster, have been developed by simply changing the solvent evaporation conditions. All three systems have retained the same phase and polydispersity of primary particles. Magnetic measurements show that the partial alignment of the easy axes of the particles in the network system due to the stacking aggregation morphology can result in significant enhancement of the coercivity and remanence values, while the opposite is obtained for the cluster system due to the random orientation of easy axes. Partial alignment in the aggregate system also results in noticeable non -monotonic field dependence of ZFC peak temperature (TpeaB). The lowest value of the blocking temperature (TB) for the cluster system is related to the lowering of the effective anisotropy due to the strongest demagnetizing effect. FC (Field cooled) memory effect was observed to be decreasing with the increasing strength of dipolar interaction of organization states. Therefore, the stacking aggregation and the cluster formation are two interesting ways of magnetic nanoparticles organization for modulating collective magnetic properties significantly, which can have renewed application potentials from recording devices to biomedicine. (C) 2016 Elsevier B.V. All rights reserved.