Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (similar to 80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.

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).

MODELING AND SIMULATION OF HYDRODYNAMIC INTERACTION OF DNA IN A MICRO-FLUIDIC CHANNEL

The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young's modulus, Poisson's ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.

Integrating biodiversity and conservation with modern agricultural landscapes

To achieve food security and meet the demands of the ever-growing human populations, farming systems have assumed unsustainable practices to produce more from a finite land area. This has been cause for concern mainly due to the often-irreversible damage done to the otherwise productive agricultural landscapes. Agro-ecology is proclaimed to be deteriorating due to eroding integrity of connected ecological mosaics and vulnerability to climate change. This has contributed to declining species diversity, loss of buffer vegetation, fragmentation of habitats, and loss of natural pollinators or predators, which eventually leads to decline in ecosystem services. Currently, a hierarchy of conservation initiatives is being considered to restore ecological integrity of agricultural landscapes. However, the challenge of identifying a suitable conservation strategy is a daunting task in view of socio-ecological factors that may constrain the choice of available strategies. One way to mitigate this situation and integrate biodiversity with agricultural landscapes is to implement offset mechanisms, which are compensatory and balancing approaches to restore the ecological health and function of an ecosystem. This needs to be tailored to the history of location specific agricultural practices, and the social, ecological and environmental conditions. The offset mechanisms can complement other initiatives through which farmers are insured against landscape-level risks such as droughts, fire and floods. For countries in the developing world with significant biodiversity and extensive agriculture, we should promote a comprehensive model of sustainable agricultural landscapes and ecosystem services, replicable at landscape to regional scales. Arguably, the model can be a potential option to sustain the integrity of biodiversity mosaic in agricultural landscapes.

Using intra-flock association patterns to understand why birds participate in mixed-species foraging flocks in terrestrial habitats

Bird species are hypothesized to join mixed-species flocks (flocks hereon) either for direct foraging or anti-predation-related benefits. In this study, conducted in a tropical evergreen forest in the Western Ghats of India, we used intra-flock association patterns to generate a community-wide assessment of flocking benefits for different species. We assumed that individuals needed to be physically proximate to particular heterospecific individuals within flocks to obtain any direct foraging benefit (flushed prey, kleptoparasitism, copying foraging locations). Alternatively, for anti-predation benefits, physical proximity to particular heterospecifics is not required, i.e. just being in the flock vicinity can suffice. Therefore, we used choice of locations within flocks to infer whether individual species are obtaining direct foraging or anti-predation benefits. A small subset of the bird community (5/29 species), composed of all members of the sallying guild, showed non-random physical proximity to heterospecifics within flocks. All preferred associates were from non-sallying guilds, suggesting that the sallying species were likely obtaining direct foraging benefits either in the form of flushed or kleptoparasitized prey. The majority of the species (24/29) chose locations randomly with respect to heterospecifics within flocks and, thus, were likely obtaining antipredation benefits. In summary, our study indicates that direct foraging benefits are important for only a small proportion of species in flocks and that predation is likely to be the main driver of flocking for most participants. Our findings apart, our study provides methodological advances that might be useful in understanding asymmetric interactions in social groups of single and multiple species.

Identifying Priority Areas for Conservation and Management in Diverse Tropical Forests

The high concentration of the world's species in tropical forests endows these systems with particular importance for retaining global biodiversity, yet it also presents significant challenges for ecology and conservation science. The vast number of rare and yet to be discovered species restricts the applicability of species-level modelling for tropical forests, while the capacity of community classification approaches to identify priorities for conservation and management is also limited. Here we assessed the degree to which macroecological modelling can overcome shortfalls in our knowledge of biodiversity in tropical forests and help identify priority areas for their conservation and management. We used 527 plant community survey plots in the Australian Wet Tropics to generate models and predictions of species richness, compositional dissimilarity, and community composition for all the 4,313 vascular plant species recorded across the region (>1.3 million communities (grid cells)). We then applied these predictions to identify areas of tropical forest likely to contain the greatest concentration of species, rare species, endemic species and primitive angiosperm families. Synthesising these alternative attributes of diversity into a single index of conservation value, we identified two areas within the Australian wet tropics that should be a high priority for future conservation actions: the Atherton Tablelands and Daintree rainforest. Our findings demonstrate the value of macroecological modelling in identifying priority areas for conservation and management actions within highly diverse systems, such as tropical forests.

Forest area estimation and reporting: implications for conservation, management and REDD

Periodic estimation, monitoring and reporting on area under forest and plantation types and afforestation rates are critical to forest and biodiversity conservation, sustainable forest management and for meeting international commitments. This article is aimed at assessing the adequacy of the current monitoring and reporting approach adopted in India in the context of new challenges of conservation and reporting to international conventions and agencies. The analysis shows that the current mode of monitoring and reporting of forest area is inadequate to meet the national and international requirements. India could be potentially over-reporting the area under forests by including many non-forest tree categories such as commercial plantations of coconut, cashew, coffee and rubber, and fruit orchards. India may also be under-reporting deforestation by reporting only gross forest area at the state and national levels. There is a need for monitoring and reporting of forest cover, deforestation and afforestation rates according to categories such as (i) natural/primary forest, (ii) secondary/degraded forests, (iii) forest plantations, (iv) commercial plantations, (v) fruit orchards and (vi) scattered trees.

Socio-cultural protection of endemic trees in humanised landscape

Culturally protected forest patches or sacred groves have been the integral part of many traditional societies. This age old tradition is a classic instance of community driven nature conservation sheltering native biodiversity and supporting various ecosystem functions particularly hydrology. The current work in Central Western Ghats of Karnataka, India, highlights that even small sacred groves amidst humanised landscapes serve as tiny islands of biodiversity, especially of rare and endemic species. Temporal analysis of landuse dynamics reveals the changing pattern of the studied landscape. There is fast reduction of forest cover (15.14-11.02 %) in last 20 years to meet up the demand of agricultural land and plantation programs. A thorough survey and assessment of woody endemic species distribution in the 25 km(2) study area documented presence of 19 endemic species. The distribution of these species is highly skewed towards the culturally protected patches in comparison to other land use elements. It is found that, among the 19 woody endemic species, those with greater ecological amplitude are widely distributed in the studied landscape in groves as well as other land use forms whereas, natural population of the sensitive endemics are very much restricted in the sacred grove fragments. The recent degradation in the sacred grove system is perhaps, due to weakening of traditional belief systems and associated laxity in grove protection leading to biotic disturbances. Revitalisation of traditional practices related to conservation of sacred groves can go a long way in strengthening natural ecological systems of fragile humid tropical landscape.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Distribution, Demography, and Conservation of Lion-tailed Macaques (Macaca silenus) in the Anamalai Hills Landscape, Western Ghats, India

The status of the endemic and endangered lion-tailed macaque (Macaca silenus) has not been properly assessed in several regions of the Western Ghats of southern India. We conducted a study in Parambikulam Forest Reserve in the state of Kerala to determine the distribution, demography, and status of lion-tailed macaques. We laid 5km(2) grid cells on the map of the study area (644km(2)) and made four replicated walks in each grid cell using GPS. We gathered data on lion-tailed macaque group locations, demography, and site covariates including trail length, duration of walk, proportion of evergreen forest, height of tallest trees, and human disturbance index. We also performed occupancy modeling using PRESENCE ver. 3.0. We estimated a minimum of 17 groups of macaques in these hills. Low detection and occupancy probabilities indicated a low density of lion-tailed macaques in the study area. Height of the tallest trees correlated positively whereas human disturbance and proportion of evergreen forest correlated negatively with occupancy in grid cells. We also used data from earlier studies carried out in the surrounding Anamalai Tiger Reserve and Nelliyampathy Hills to discuss the conservation status in the large Anamalai Hills Landscape. This landscape harbors an estimated population of 1108 individuals of lion-tailed macaques, which is about one third of the entire estimated wild population of this species. A conservation plan for this landscape could be used as a model for conservation in other regions of the Western Ghats.

Identifying regions for conservation of sloth bears through occupancy modelling in north-eastern Karnataka, India

In the absence of information on species in decline with contracting ranges, management should emphasize remaining populations and protection of their habitats. Threatened by anthropogenic pressure including habitat degradation and loss, sloth bears (Melursus ursinus) in India have become limited in range, habitat, and population size. We identified ecological and anthropogenic determinants of occurrence within an occupancy framework to evaluate habitat suitability of non-protected regions (with sloth bears) in northeastern Karnataka, India. We employed a systematic sampling methodology to yield presence absence data to examine a priori hypotheses of determinants that affected occupancy. These covariates were broadly classified as habitat or anthropogenic factors. Mean number of termite mounds and trees positively influenced sloth bear occupancy, and grazing pressure expounded by mean number of livestock dung affected it negatively. Also, mean percentage of shrub coverage had no impact on bear inhabitance. The best fitting model further predicted habitats in Bukkasagara, Agoli, and Benakal reserved forests to have 38%, 75%, and 88%, respectively, of their sampled grid cells with high occupancies (>0.70) albeit little or no legal protection. We recommend a conservation strategy that includes protection of vegetation stand-structure, maintenance of soil moisture, and enrichment of habitat for the long-term welfare of this species.

Conservation Properties of the Trapezoidal Rule in Linear Time Domain Analysis of Acoustics and Structures

The trapezoidal rule, which is a special case of the Newmark family of algorithms, is one of the most widely used methods for transient hyperbolic problems. In this work, we show that this rule conserves linear and angular momenta and energy in the case of undamped linear elastodynamics problems, and an ``energy-like measure'' in the case of undamped acoustic problems. These conservation properties, thus, provide a rational basis for using this algorithm. In linear elastodynamics problems, variants of the trapezoidal rule that incorporate ``high-frequency'' dissipation are often used, since the higher frequencies, which are not approximated properly by the standard displacement-based approach, often result in unphysical behavior. Instead of modifying the trapezoidal algorithm, we propose using a hybrid finite element framework for constructing the stiffness matrix. Hybrid finite elements, which are based on a two-field variational formulation involving displacement and stresses, are known to approximate the eigenvalues much more accurately than the standard displacement-based approach, thereby either bypassing or reducing the need for high-frequency dissipation. We show this by means of several examples, where we compare the numerical solutions obtained using the displacement-based and hybrid approaches against analytical solutions.

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Ser/Thr and Tyr protein kinases orchestrate many signalling pathways and hence loss in this balance leads to many disease phenotypes. Due to their high abundance, diversity and importance, efforts have been made in the past to classify kinases and annotate their functions at both gross and fine levels. These kinases are conventionally classified into subfamilies based on the sequences of catalytic domains. Usually the domain architecture of a full-length kinase is consistent with the subfamily classification made based on the sequence of kinase domain. Important contributions of modular domains to the overall function of the kinase are well known. Recently occurrence of two kinds of outlier kinases-''Hybrid'' and ``Rogue'' has been reported. These show considerable deviations in their domain architectures from the typical domain architecture known for the classical kinase subfamilies. This article provides an overview of the different subfamilies of human kinases and the role of non-kinase domains in functions and diseases. Importantly this article provides analysis of hybrid and rogue kinases encoded in the human genome and highlights their conservation in closely related primate species. These kinases are examples of elegant rewiring to bring about subtle functional differences compared to canonical variants.