Choosing an appropriate index to construct dominance hierarchies in animal societies: a comparison of three indices

A plethora of indices have been proposed and used to construct dominance hierarchies in a variety of vertebrate and invertebrate societies, although the rationale for choosing a particular index for a particular species is seldom explained. In this study, we analysed and compared three such indices, viz Clutton-Brock et al.'s index (CBI), originally developed for red deer, Cervus elaphus, David's score (DS) originally proposed by the statistician H. A. David and the frequency-based index of dominance (FDI) developed and routinely used by our group for the primitively eusocial wasps Ropalidia marginata and Ropalidia cyathiformis. Dominance ranks attributed by all three indices were strongly and positively correlated for both natural data sets from the wasp colonies and for artificial data sets generated for the purpose. However, the indices differed in their ability to yield unique (untied) ranks in the natural data sets. This appears to be caused by the presence of noninteracting individuals and reversals in the direction of dominance in some of the pairs in the natural data sets. This was confirmed by creating additional artificial data sets with noninteracting individuals and with reversals. Based on the criterion of yielding the largest proportion of unique ranks, we found that FDI is best suited for societies such as the wasps belonging to Ropalidia, DS is best suited for societies with reversals and CBI remains a suitable index for societies such as red deer in which multiple interactions are uncommon. (C) 2009 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Governing the local networks in Indian agrarian societies-an MAS perspective

In a networked society, governing advocacy groups and networks through decentralized systems of policy implementation has been the interest of governance network literature. This paper addresses the topic of governing networks in the context of Indian agrarian societies by taking the case example of a welfare scheme for the Indian rural poor. We explore context-specific regulatory dynamics through the situated agent based architectural framework. The effects of various regulatory strategies that can be adopted by governing node are tested under various action arenas through experimental design. Results show the impact of regulatory strategies on the resource dependencies and asymmetries in the network relationships. This indicates that the optimal feasible regulatory strategy in networked society is institutionally rational and is context dependent. Further, we show that situated MAS architecture is a natural fit for institutional understanding of the dynamics (Ostrom et al. in Rules, games, and common-pool resources, 1994).

Importance of amino-terminus in maintenance of oligomeric structure of cytosolic serine hydroxymethyltransferase

The role of the amino and carboxyl-terminal regions of cytosolic serine hydroxymethyltransferase (SHMT) in subunit assembly and catalysis was studied using six amino-terminal (lacking the first 6, 14, 30, 49, 58, and 75 residues) and two carboxyl-terminal (lacking the last 49 and 185 residues) deletion mutants. These mutants were constructed from a full length cDNA clone using restriction enzyme/PCR-based methods and overexpressed in Escherichia coli. The overexpressed proteins, des-(A1-K6)-SHMT and des-(A1- W14)-SHMT were present in the soluble fraction and they were purified to homogeneity. The deletion clones, for des-(A1–V30)-SHMT and des-(A1–L49)-SHMT were expressed at very low levels, whereas des-(A1–R58)-SHMT, des-(A1–G75)-SHMT, des-(Q435–F483)-SHMT and des-(L299-F483)-SHMT mutant proteins were not soluble and formed inclusion bodies. Des-(A1–K6)-SHMT and des-(A1–W14)-SHMT catalyzed both the tetrahydrofolate-dependent and tetrahydrofolate-independent reactions, generating characteristic spectral intermediates with glycine and tetrahydrofolate. The two mutants had similar kinetic parameters to that of the recombinant SHMT (rSHMT). However, at 55 °C, the des-(A1–W14)-SHMT lost almost all the activity within 5 min, while at the same temperature rSHMT and des-(A1–K6)-SHMT retained 85% and 70% activity, respectively. Thermal denaturation studies showed that des-(A1–W14)-SHMT had a lower apparent melting temperature (52°C) compared to rSHMT (56°C) and des-(A1–K6)-SHMT (55 °C), suggesting that N-terminal deletion had resulted in a decrease in the thermal stability of the enzyme. Further, urea induced inactivation of the enzymes revealed that 50% inactivation occurred at a lower urea concentration (1.2 ± 0.1 M) in the case of des-(A1–W14)-SHMT compared to rSHMT (1.8 ±0.1 M) and des-(A1–K6)-SHMT (1.7 ±0.1 M). The apoenzyme of des-(A1- W14)-SHMT was present predominantly in the dimer form, whereas the apoenzymes of rSHMT and des-(A1–K6)-SHMT were a mixture of tetramers (≈75% and ≈65%, respectively) and dimers. While, rSHMT and des-(A1–K6)-SHMT apoenzymes could be reconstituted upon the addition of pyridoxal-5'-phosphate to 96% and 94% enzyme activity, respectively, des-(A1–W14)-SHMT apoenzyme could be reconstituted only upto 22%. The percentage activity regained correlated with the appearance of visible CD at 425 nm and with the amount of enzyme present in the tetrameric form upon reconstitution as monitored by gel filtration. These results demonstrate that, in addition to the cofactor, the N-terminal arm plays an important role in stabilizing the tetrameric structure of SHMT.

Cultural-Evolution of Ecological Prudence

Animals often behave in a profligate fashion and decimate the populations of plants and animals they depend upon. They may, however, evolve prudent behaviour under special conditions, namely when such prudence greatly enhances the success of populations that are not too prone to invasions by profligate individuals. Cultural evolution in human societies can also lead to the adoption of prudent practices under similar conditions. These are more likely to be realized in stable environments in which the human populations tend to grow close to the carrying capacity, when the human groups are closed, and when the technology is stagnant. These conditions probably prevailed in the hunter—gatherer societies of the tropics and subtropics, and led to the adoption of a number of socially imposed restraints on the use of plant and animal resources. Such practices were rationalized in the form of Nature-worship. The Indian caste society became so organized as to fulfill these conditions, and gave rise to two religions, Buddhism and Jainism, which emphasize compassion towards all forms of life. The pastoral nomads of the middle east, on the other hand, lived in an environment which militated against prudence, and these societies gave rise to religions like Christianity, which declared war on nature. As the ruling elite and state have grown in power, they have tried to wrest control of natural resources from the local communities. This has sometimes resulted in conservation and prudent use under guidance from the state, but has often led to conflicts with local populations to the detriment of prudent behaviour. Modern technological progress has also often removed the need for conservation, as when availability of coal permitted the deforestation of England. While modern scientific understanding has led to a better appreciation of the need for prudence, the prevailing social and economic conditions often militate against any implementation of the understanding, as is seen from the history of whaling. However, the imperative for survival of the poor from the Third-World countries may finally bring about conditions in which ecological prudence may once again come to dominate human cultures as it might once have done with stable societies of hunter—gatherers.

On the moulding of population viscosity by natural selection

In this paper, we explore the conjoint evolution of dispersal and social behaviour. The model investigated is of a population distributed over a number of sites each with a carrying capacity of two adults and an episode of dispersal in the juvenile stage. The fertilities are governed by whether an individual and its neighbour are selfish or co-operative. It is shown that the best dispersal strategy for the co-operative genotype always involves lower levels of dispersal; and further that ecological conditions favouring low levels of dispersal increase the selective advantage of a co-operative genotype. Given this positive feedback, we suggest that in any taxon viscosity and co-operativity will tend to be correlated and bimodally distributed. Hence we predict the existence of two kinds of animal societies; viscous and co-operative (e.g. quasi-social wasps such as Mischocyttarus), and non-viscous and selfish (e.g. communal sphecid wasps such as Cerceris), and relatively few social groups with intermediate levels of co-operativity and viscosity. We also suggest that when one of the two sexes disperses, it will be the sex with lower potential for co-operative behaviour.

Interrogating an insect society

Insect societies such as those of ants, bees, and wasps consist of 1 or a small number of fertile queens and a large number of sterile or nearly sterile workers. While the queens engage in laying eggs, workers perform all other tasks such as nest building, acquisition and processing of food, and brood care. How do such societies function in a coordinated and efficient manner? What are the rules that individuals follow? How are these rules made and enforced? These questions are of obvious interest to us as fellow social animals but how do we interrogate an insect society and seek answers to these questions? In this article I will describe my research that was designed to see answers from an insect society to a series of questions of obvious interest to us. I have chosen the Indian paper wasp Ropalidia marginata for this purpose, a species that is abundantly distributed in peninsular India and serves as an excellent model system. An important feature of this species is that queens and workers are morphologically identical and physiologically nearly so. How then does an individual become a queen? How does the queen suppress worker reproduction? How does the queen regulate the nonreproductive activities of the workers? What is the function of aggression shown by different individuals? How and when is the queen's heir decided? I will show how such questions can indeed be investigated and will emphasize the need for a whole range of different techniques of observation and experimentation.

New measures for estimating surface complementarity and packing at protein-protein interfaces

A number of methods exist that use different approaches to assess geometric properties like the surface complementarity and atom packing at the protein-protein interface. We have developed two new and conceptually different measures using the Delaunay tessellation and interface slice selection to compute the surface complementarity and atom packing at the protein-protein interface in a straightforward manner. Our measures show a strong correlation among themselves and with other existing measures, and can be calculated in a highly time-efficient manner. The measures are discriminative for evaluating biological, as well as non-biological protein-protein contacts, especially from large protein complexes and large-scale structural studies(http://pallab.serc. iisc.ernet.in/nip_nsc). (C) 201 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

Identification of protein interaction regions of VINC/NEAT1/Men epsilon RNA

The virus inducible non-coding RNA (VINC) was detected initially in the brain of mice infected with Japanese encephalitis virus (JEV) and rabies virus. VINC is also known as NEAT1 or Men epsilon RNA. It is localized in the nuclear paraspeckles of several murine as well as human cell lines and is essential for paraspeckle formation. We demonstrate that VINC interacts with the paraspeckle protein, P54nrb through three different protein interaction regions (PIRs) one of which (PIR-1) is localized near the 50 end while the other two (PIR-2, PIR-3) are localized near the 30 region of VINC. Our studies suggest that VINC may interact with P54nrb through a novel mechanism which is different from that reported for protein coding RNAs. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips

The crystal structure of beta-hydroxyacyl acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) has been determined at a resolution of 2.4 angstrom. PfFabZ has been found to exist as a homodimer (d-PfFabZ) in the crystals of the present study in contrast to the reported hexameric form (h-PfFabZ) which is a trimer of dimers crystallized in a different condition. The catalytic sites of this enzyme are located in deep narrow tunnel-shaped pockets formed at the dimer interface. A histidine residue from one subunit of the dimer and a glutamate residue from the other subunit lining the tunnel form the catalytic dyad in the reported crystal structures. While the position of glutamate remains unaltered in the crystal structure of d-PffabZ compared to that in b-PfFabZ, the histidine residue takes up an entirely different conformation and moves away from the tunnel leading to a His-Phe cis-trans peptide flip at the histidine residue. In addition, a loop in the vicinity has been observed to undergo a similar flip at a Tyr-Pro peptide bond. These alterations not only prevent the formation of a hexamer but also distort the active site geometry resulting in a dimeric form of FabZ that is incapable of substrate binding. The dimeric state and an altered catalytic site architecture make d-PfFabZ distinctly different from the FabZ structures described so far. Dynamic light scattering and size exclusion chromatographic studies clearly indicate a pH-related switching of the dimers to active hexamers. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserv.

A spectroscopic study of the interaction of isoflavones with human serum albumin

Genistein and daidzein, the major isoflavones present in soybeans, possess a wide spectrum of physiological and pharmacological functions. The binding of genistein to human serum albumin (HSA) has been investigated by equilibrium dialysis, fluorescence measurements, CD and molecular visualization. One mole of genistein is bound per mole of HSA with a binding constant of 1.5 +/- 0.2 X 10(5) m(-1). Binding of genistein to HSA precludes the attachment of daidzein. The ability of HSA to bind genistein is found to be lost when the tryptophan residue of albumin is modified with N-bromosuccinimide. At 27 degrees C (pH 7.4), van't Hoff's enthalpy, entropy and free energy changes that accompany the binding are found to be -13.16 kcal.mol(-1), -21 cal.mol(-1)K(-1) and -6.86 kcal.mol(-1), respectively. Temperature and ionic strength dependence and competitive binding measurements of genistein with HSA in the presence of fatty acids and 8-anilino-1-naphthalene sulfonic acid have suggested the involvement of both hydrophobic and ionic interactions in the genistein-HSA binding. Binding measurements of genistein with BSA and HSA, and those in the presence of warfarin and 2,3,5-tri-iodobenzoic acid and Forster energy transfer measurements have been used for deducing the binding pocket on HSA. Fluorescence anisotropy measurements of daidzein bound and then displaced with warfarin, 2,3,5-tri-iodobenzoic acid or diazepam confirm the binding of daidzein and genistein to subdomain IIA of HSA. The ability of HSA to form ternery complexes with other neutral molecules such as warfarin, which also binds within the subdomain IIA pocket, increases our understanding of the binding dynamics of exogenous drugs to HSA.

Functional linkages can reveal protein complexes for structure determination

The study of molecular machines, and protein complexes in general, is a growth area of biology. Is there a computational method for inferring which combinations of proteins in an organism are likely to form a crystallizable complex? We use the Protein Data Bank (PDB) to assess the usefulness of inferred functional protein linkages for this task. We find that of 242 nonredundant prokaryotic protein complexes (complexes excluding structural variants of the same protein) from organisms that are shared between the current PDB and the Prolinks functional linkage database, 44% (107/242) contain proteins that are linked at high-confidence by one or more methods of computed functional linkages. This suggests that computing functional linkages will be useful in defining protein complexes for structural studies. We offer a database of such inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archea.

Social Life of Captive Asian Elephants (Elephas maximus) in Southern India: Implications for Elephant Welfare

Asian elephants in the wild live in complex social societies; in captivity, however, management often occurs in solitary conditions, especially at the temples and private places of India. To investigate the effect of social isolation, this study assessed the social group sizes and the presence of stereotypies among 140 captive Asian elephants managed in 3 captive systems (private, temple, and forest department) in Tamil Nadu, India, between 2003 and 2005. The majority of the facilities in the private (82%) and temple (95%) systems held a single elephant without opportunity for social interaction. The forest department managed the elephants in significantly larger groups than the private and temple systems. Among the 3 systems, the proportion of elephants with stereotypies was the highest in temple (49%) followed by private system (26%) and the forest department facility (6%); this correlates with the social isolation trend observed in the 3 systems and suggests a possible link between social isolation and abnormal elephant behavior separate from other environmental factors. The results of this study indicate it would be of greater benefit to elephant well being to keep the patchily distributed solitary temple and private elephants who are socially compatible and free from contagious diseases in small social groups at ocommon elephant houseso for socialization.

Structure and activity cyclase activated of OK-GC: A kidney receptor-guanylate cyclase activated by guanylin peptides

Uroguanylin, guanylin, and lymphoguanylin are small peptides that activate renal and intestinal receptor guanylate cyclases (GC). They are structurally similar to bacterial heat-stable enterotoxins (ST) that cause secretory diarrhea. Uroguanylin, guanylin, and ST elicit natriuresis, kaliuresis, and diuresis by direct actions on kidney GC receptors. A 3,762-bp cDNA characterizing a uroguanylin/guanylin/ST receptor was isolated from opossum kidney (OK) cell RNA/cDNA. This kidney cDNA (OK-GC) encodes a mature protein containing 1,049 residues sharing 72.4�75.8% identity with rat, human, and porcine forms of intestinal GC-C receptors. COS or HEK-293 cells expressing OK-GC receptor protein were activated by uroguanylin, guanylin, or ST13 peptides. The 3.8-kb OK-GC mRNA transcript is most abundant in the kidney cortex and intestinal mucosa, with lower mRNA levels observed in urinary bladder, adrenal gland, and myocardium and with no detectable transcripts in skin or stomach mucosa. We propose that OK-GC receptor GC participates in a renal mechanism of action for uroguanylin and/or guanylin in the physiological regulation of urinary sodium, potassium, and water excretion. This renal tubular receptor GC may be a target for circulating uroguanylin in an endocrine link between the intestine and kidney and/or participate in an intrarenal paracrine mechanism for regulation of kidney function via the intracellular second messenger, cGMP.