Isolation and characterization of some new formate utilizing bacteria

Five isolates degrading and assimilating foramte were isolated from chicken dung. Characterization indicated two differents types. One of these belonged to the genus Alcaligenes and assimilated formate autotrophically. The other four isolates were identical, belongedto hte genus Protaminobacter and assimilated formate heterotrophicaly by the serine pathway.

Evolution, Homology Conservation, and Identification of Unique Sequence Signatures in GH19 Family Chitinases

The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

Background: The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly in pathogens, not only for a better understanding of the pathogen biology, but also for identifying drug targets and the minimal gene set for the organism. Essentiality is inherently a systems property and requires consideration of the system as a whole for their identification. The available experimental approaches capture some aspects but each method comes with its own limitations. Moreover, they do not explain the basis for essentiality in most cases. A powerful prediction method to recognize this gene pool including rationalization of the known essential genes in a given organism would be very useful. Here we describe a multi-level multi-scale approach to identify the essential gene pool in a deadly pathogen, Mycobacterium tuberculosis. Results: The multi-level workflow analyses the bacterial cell by studying (a) genome-wide gene expression profiles to identify the set of genes which show consistent and significant levels of expression in multiple samples of the same condition, (b) indispensability for growth by using gene expression integrated flux balance analysis of a genome-scale metabolic model, (c) importance for maintaining the integrity and flow in a protein-protein interaction network and (d) evolutionary conservation in a set of genomes of the same ecological niche. In the gene pool identified, the functional basis for essentiality has been addressed by studying residue level conservation and the sub-structure at the ligand binding pockets, from which essential amino acid residues in that pocket have also been identified. 283 genes were identified as essential genes with high-confidence. An agreement of about 73.5% is observed with that obtained from the experimental transposon mutagenesis technique. A large proportion of the identified genes belong to the class of intermediary metabolism and respiration. Conclusions: The multi-scale, multi-level approach described can be generally applied to other pathogens as well. The essential gene pool identified form a basis for designing experiments to probe their finer functional roles and also serve as a ready shortlist for identifying drug targets.

Study of effects of dopants on structure of vitreous semiconductors (GeSe3.5)100-xMx (M = Bi, Sb) using high pressure techniques

An investigation of the problem of controlled doping of amorphous chalcogenide semiconductors utilizing a Bridgman anvil high pressure technique, has been undertaken. Bulk amorphous semiconducting materials (GeSe3.5)100-x doped with M = Bi (x = 2, 4, 10) and M = Sb (x = 10) respectively are studied up to a pressure of 100 kbar down to liquid nitrogen temperature, with a view to observe the impurity induced modifications. Measurement of the electrical conductivity of the doped samples under quasi-hydrostatic pressure reveals that the pressure induced effects in lightly doped (2 at % Bi) and heavily doped (x = 4, 10) semiconductors are markedly different. The pressure effects in Sb-doped semiconductors are quite different from those in Bi-doped material.

An enzymic approach to the study of sewage and sludges

The purpose of the work described here has been (a) to obtain some evidence on catalase (an oxidative enzyme) and protease, urease and phosphatase (hydrolytic enzymes) in sewage, activated sludge and septic tank sludge, and (b) to use this evidence, as a new approach, to find out the relationship between the main groups of the micro-organisms (bacteria and protozoa) and their relative influence on the purification process. To make a rapid assessment of the enzyme activities in these systems in the course of three weeks, as an experimental measure, rat tissues were added, which might serve as an additional or a ‘shock’ load of organic matter to follow broadly the development of bacteria and protozoa and the changes in the enzyme activities in the different systems. A control system with sewage alone was also run. The results showed that the initial decomposition of the fresh organic matter added to sewage and sludges was almost entirely due to bacterial activity and the later oxidative changes and removal of the suspended solids, including the bacteria, were largely due to the protozoa, such as Epistylis articulata. Analysis of the enzyme activities in the different materials showed, among other things, that the activated sludge, with its mized bacteria, protozoa and other organisms, as a whole, contained about twenty times more protease activity than an equivalent amount of the protozoan E. articulata, and that this protozoan contained five times more catalase activity than the activated sludge. The significance of these observations is discussed.

An ethnobotanical study of traditional anti-inflammatory plants used by the Lohit community of Arunachal Pradesh, India

Aim of the study: Most people especially in rural areas depend on herbal medicines to treat many diseases including inflammation-related ailments such as rheumatism, muscle swelling, cut wound, accidental bone fracture, insect bites, pains and burn by fire and hot water. The objectives of this study were: to catalog ethno-medicinal plants of Lohit community, ecological status, indigenous folk medicinal uses, morphological parts used and to determine their reported pharmacological studies. Materials and methods: The ethnobotanical information on traditional medicinal plants exclusively used for management of inflammation-related ailments by the Khampti community of Arunachal Pradesh, India was based on first-hand field survey work through semi-structured interviews. Results and conclusion: A total of 34 species in 32 genera and 22 families were encountered during the field survey. Botanical families such as Asteraceae, Euphorbiaceae, Zingiberaceae and Lamiaceae were represented by the highest numbers of species reported in this study. Thirteen plant species, namely: Bombax ceiba, Canarium strictum, Chloranthus erectus, Xanthium indicum, Lycopodium clavatum, Coleus blumei, Batrachospermum atrum, Chlorella vulgaris, Marchantia palmata, Marchantia polymorpha, Eria pannea, Sterculia villosa and Alpinia galanga are reported for the first time for the treatment of inflammation-related diseases.

Conserving Biodiversity as If People Matter: A Case Study from India

India has rich traditions of nature conservation as well as a vigorous official program of protection of nature reserves developed over the last 40 years. However, the officialp rograms uffers fromt otal relianceo n authoritarianm anagement arrangements in which decisions are made centrally and coercion is used to implement them. At the same time, the state apparatus organises subsidized resource flows to the urbanindustrial- intensivea griculturalc omplex which promote inefficient,n on-sustainable resource-use patterns that are inimical to conservation of biodiversity. These processes are illustrated within the concrete setting of the district of Uttara Kannada in southern India. It is suggested that the interests of conservation would be served far better by an approach that withdraws the subsidies to the elite so that a much more efficient, sustainable and equitable pattern of resource use, compatible with conservation of biodiversity, can be instituted. In conjunction with this, the larger society should involve local people in working out detailed plans for conservation of biodiversity and offer them adequate authority as well as appropriate financial incentives to implement these plans. The paper goes on to illustrate how such an approach may be implemented in the case of Uttara Kannada.

The Consequences of Phenotypic Plasticity in Cyclically Varying Environments: A Genetic Algorithm Study

By “phenotypic plasticity” we refer to the capacity of a genotype to exhibit different phenotypes, whether in the same or in different environments. We have previously demonstrated that phenotypic plasticity can improve the degree of adaptation achieved via natural selection (Behera & Nanjundiah, 1995). That result was obtained from a genetic algorithm model of haploid genotypes (idealized as one-dimensional strings of genes) evolving in a fixed environment. Here, the dynamics of evolution is examined under conditions of a cyclically varying environment. We find that the rate of evolution, as well as the extent of adaptation (as measured by mean population fitness) is lowered because of environmental cycling. The decrease is adaptation caused by a varying environment can, however, be partly or wholly compensated by an increase in the degree of plasticity that a genotype is capable of. Also, the reduction of population fitness caused by a variable environment can be partially offset by decreasing the total number of genetic loci. We conjecture that an increase in genome size may have been among the factors responsible for the evolution of phenotypic plasticity.

Location of Pathogenic Bacteria during Persistent Infections: Insights from an Analysis Using Game Theory

Bacterial persistent infections are responsible for a significant amount of the human morbidity and mortality. Unlike acute bacterial infections, it is very difficult to treat persistent bacterial infections (e.g. tuberculosis). Knowledge about the location of pathogenic bacteria during persistent infection will help to treat such conditions by designing novel drugs which can reach such locations. In this study, events of bacterial persistent infections were analyzed using game theory. A game was defined where the pathogen and the host are the two players with a conflict of interest. Criteria for the establishment of Nash equilibrium were calculated for this game. This theoretical model, which is very simple and heuristic, predicts that during persistent infections pathogenic bacteria stay in both intracellular and extracellular compartments of the host. The result of this study implies that a bacterium should be able to survive in both intracellular and extracellular compartments of the host in order to cause persistent infections. This explains why persistent infections are more often caused by intracellular pathogens like Mycobacterium and Salmonella. Moreover, this prediction is in consistence with the results of previous experimental studies.

Middle aged wasps mate through most of the year, without regard to body size, ovarian development and nestmateship: a laboratory study of the primitively eusocial wasp Ropalidia marginata

We studied the mating behaviour of the primi-tively eusocial wasp Ropalidia marginata and the factors that may influence sperm transfer. By introducing a male and a female R. marginata into ventilated transparent plastic boxes, we were able to observe mating behaviour, and it involved mounting and short or long conjugation of the wasps. Dissection of female wasps after the observation indicated that long conjugation is a good behavioural predictor of sperm transfer. This finding makes it possible to obtain mated females without dissecting them every time. We tested the effect of age, season, relatedness, body size and female's ovarian status on mating. Under laboratory conditions, mating success declined rapidly below and above the ages 5-20 days. Within this age range mating success was significantly low in December compared to other months tested. There was no nestmate discrimination, and there was no influence of male and female body size or of the ovarian state of the female on the probability of sperm transfer.

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.

Relationship between annual rainfall and tree mortality in a tropical dry forest: Results of a 19-year study at Mudumalai, southern India

Variability in rainfall is known to be a major influence on the dynamics of tropical forests, especially rates and patterns of tree mortality. In tropical dry forests a number of contributing factors to tree mortality, including dry season fire and herbivory by large herbivorous mammals, could be related to rainfall patterns, while loss of water potential in trees during the dry season or a wet season drought could also result in enhanced rates of death. While tree mortality as influenced by severe drought has been examined in tropical wet forests there is insufficient understanding of this process in tropical dry forests. We examined these causal factors in relation to inter-annual differences in rainfall in causing tree mortality within a 50-ha Forest Dynamics Plot located in the tropical dry deciduous forests of Mudumalai, southern India, that has been monitored annually since 1988. Over a 19-year period (1988-2007) mean annual mortality rate of all stems >1 cm dbh was 6.9 +/- 4.6% (range = 1.5-17.5%); mortality rates broadly declined from the smaller to the larger size classes with the rates in stems >30 cm dbh being among the lowest recorded in tropical forest globally. Fire was the main agent of mortality in stems 1-5 cm dbh, elephant-herbivory in stems 5-10 cm dbh, and other natural causes in stems > 10 cm dbh. Elephant-related mortality did not show any relationship to rainfall. On the other hand, fire-related mortality was significantly negatively correlated to quantity of rainfall during the preceding year. Mortality due to other causes in the larger stem sizes was significantly negatively correlated to rainfall with a 2-3-year lag, suggesting that water deficit from mild or prolonged drought enhanced the risk of death but only with a time lag that was greater than similar lags in tree mortality observed in other forest types. In this respect, tropical dry forests growing in regions of high rainfall variability may have evolved greater resistance to rainfall deficit as compared to tropical moist or temperate forests but are still vulnerable to drought-related mortality.

Assessing the mitigation potential of forestry activities in a changing climate: A case study for Karnataka

The Clean Development Mechanism (CDM), Article 12 of the Kyoto Protocol allows Afforestation and Reforestation (A/R) projects as mitigation activities to offset the CO2 in the atmosphere whilst simultaneously seeking to ensure sustainable development for the host country. The Kyoto Protocol was ratified by the Government of India in August 2002 and one of India's objectives in acceding to the Protocol was to fulfil the prerequisites for implementation of projects under the CDM in accordance with national sustainable priorities. The objective of this paper is to assess the effectiveness of using large-scale forestry projects under the CDM in achieving its twin goals using Karnataka State as a case study. The Generalized Comprehensive Mitigation Assessment Process (GCOMAP) Model is used to observe the effect of varying carbon prices on the land available for A/R projects. The model is coupled with outputs from the Lund-Potsdam-Jena (LPJ) Dynamic Global Vegetation Model to incorporate the impacts of temperature rise due to climate change under the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emissions Scenarios (SRES) A2, A1B and B1. With rising temperatures and CO2, vegetation productivity is increased under A2 and A1B scenarios and reduced under B1. Results indicate that higher carbon price paths produce higher gains in carbon credits and accelerate the rate at which available land hits maximum capacity thus acting as either an incentive or disincentive for landowners to commit their lands to forestry mitigation projects. (C) 2009 Elsevier B.V. All rights reserved.

Microbially induced separation of quartz from hematite using sulfate reducing bacteria

Cells and metabolic products of Desulfovibrio desulfuricans were successfully used to separate quartz from hematite through environmentally benign microbially induced flotation. Bacterial metabolic products such as extracellular proteins and polysaccharides were isolated from both unadapted and mineral-adapted bacterial metabolite and their basic characteristics were studied in order to get insight into the changes brought about on bioreagents during adaptation. Interaction between bacterial cells and metabolites with minerals like hematite and quartz brought about significant surface-chemical changes on both the minerals. Quartz was rendered more hydrophobic, while hematite became more hydrophilic after biotreatment.The predominance of bacterial polysaccharides on interacted hematite and of proteins on quartz was responsible for the above surface-chemical changes, as attested through adsorption studies. Surface-chemical changes were also observed on bacterial cells after adaptation to the above minerals. Selective separation of quartz from hematite was achieved through interaction with quartz-adapted bacterial cells and metabolite. Mineral-specific proteins secreted by quartz-adapted cells were responsible for conferment of hydrophobicity on quartz resulting in enhanced separation from hematite through flotation. (C) 2010 Elsevier B.V. All rights reserved.