Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.

Stable carbon isotope ratios in Asian elephant collagen: implications for dietary studies

Stable carbon isotope ratios in bone collagen have been used in a variety of dietary studies in modern and fossil animals, including humans. Inherent in the stable isotope technique is the assumption that the isotopic signature is a reflection of the diet and is persistent in collagen because this is a relatively inert protein. Carbon isotope analyses of bones from a southern Indian population of Asian elephant (Elephas maximus), a long-lived mammal that alternates seasonally between a predominantly C3 (browse) and C4 (grass) plant diet, showed two patterns that have important implications for dietary interpretation based on isotopic studies. Relative to the quantity of the two plant types consumed on average, the ?13C signal in collagen indicated that more carbon was incorporated from C3 plants, possibly due to their higher protein contribution. There was a much greater variance in ?13C values of collagen in sub-adult (range -10.5� to-22.7�, variance=14.51) compared to adult animals (range -16.0� to -20.3�, variance=1.85) pointing to high collagen turnover rates and non-persistent isotopic signatures in younger, growing animals. It thus seems important to correct for any significant relative differences in nutritive value of food types and also consider the age of an animal before drawing definite conclusions about its diet from isotope ratios.

Implications of the recent high statistics determination of the pion electromagnetic form factor in the timelike region

The recently evaluated two-pion contribution to the muon g - 2 and the phase of the pion electromagnetic form factor in the elastic region, known from pi pi scattering by Fermi-Watson theorem, are exploited by analytic techniques for finding correlations between the coefficients of the Taylor expansion at t = 0 and the values of the form factor at several points in the spacelike region. We do not use specific parametrizations, and the results are fully independent of the unknown phase in the inelastic region. Using for instance, from recent determinations, < r(pi)(2)> = (0.435 +/- 0.005) fm(2) and F(-1.6 GeV2) = 0.243(-0.014)(+0.022), we obtain the allowed ranges 3.75 GeV-4 less than or similar to c less than or similar to 3.98 GeV-4 and 9.91 GeV-6 less than or similar to d less than or similar to 10.46 GeV-6 for the curvature and the next Taylor coefficient, with a strong correlation between them. We also predict a large region in the complex plane where the form factor cannot have zeros.

Potential and economics of forestry options for carbon sequestration in India

There is a need to understand the carbon (C) sequestration potential of the forestry option and its financial implications for each country.In India the C emissions from deforestation are estimated to be nearly offset by C sequestration in forests under succession and tree plantations. India has nearly succeeded in stabilizing the area under forests and has adequate forest conservation strategies. Biomass demands for softwood, hardwood and firewood are estimated to double or treble by the year 2020. A set of forestry options were developed to meet the projected biomass needs, and keeping in mind the features of land categories available, three scenarios were developed: potential; demand-driven; and programme-driven scenarios. Adoption of the demand-driven scenario, targeted at meeting the projected biomass needs, is estimated to sequester 78 Mt of C annually after accounting for all emissions resulting from clearfelling and end use of biomass. The demand-driven scenario is estimated to offset 50% of national C emission at 1990 level. The cost per t of C sequestered for forestry options is lower than the energy options considered. The annual investment required for implementing the demand-driven scenario is estimated to be US$ 2.1 billion for six years and is shown to be feasible. Among forestry options, the ranking based on investment cost per t of C sequestered from least cost to highest cost is; natural regeneration-agro-forestry-enhanced natural regeneration (< US$ 2.5/t C)-timber-community-softwood forestry (US$ 3.3 to 7.3 per t of C).

The precision of regulation in Dictyostelium discoideum: implications for cell-type proportioning in the absence of spatial pattern

We have made careful counts of the exact number of spore, stalk and basal disc cells in small fruiting bodies of Dictyostelium discoideum (undifferentiated amoebae are found only rarely and on average their fraction is 4.96 x 10(-4)). (i) Within aggregates of a given size, the relative apportioning of amoebae to the main cell types occurs with a remarkable degree of precision. In most cases the coefficient of variation (c.v.) in the mean fraction of cells that form spores is within 4.86%. The contribution of stalk and basal disc cells is highly variable when considered separately (c.v.'s upto 25% and 100%, respectively), but markedly less so when considered together. Calculations based on theoretical models indicate that purely cell-autonomous specification of cell, fate cannot account for die observed accuracy of proportioning. Cell-autonomous determination to a prestalk or prespore condition followed by cell type interconversion, and stabilised by feedbacks, suffices to explain the measured accuracy. (ii) The fraction of amoebae that differentiates into spores increases monotonically with the total number of cells. This fraction rises from an average of 73.6% for total cell numbers below 30 and reaches 86.0% for cell numbers between 170 and 200 (it remains steady thereafter at around 86%). Correspondingly, the fraction of amoebae differentiating into stalk or basal disc decreases viith total size. These trends are in accordance with evolutionary expectations and imply that a mechanism for sensing the overall size of the aggregate also plays an essential role in the determination of cell-type proportions.

Escape of high mass ions due to initial thermal energy and its implications for axially symmetric RF ion trap mass analyzer design

This paper investigates the loss of high mass ions due to their initial thermal energy in ion trap mass analyzers. It provides an analytical expression for estimating the percentage loss of ions of a given mass at a particular temperature, in a trap operating under a predetermined set of conditions. The expression we developed can be used to study the loss of ions due to its initial thermal energy in traps which have nonlinear fields as well as those which have linear fields. The expression for the percentage of ions lost is shown to be a function of the temperature of the ensemble of ions, ion mass and ion escape velocity. An analytical expression for the escape velocity has also been derived in terms of the trapping field, drive frequency and ion mass. Because the trapping field is determined by trap design parameters and operating conditions, it has been possible to study the influence of these parameters on ion loss. The parameters investigated include ion temperature, magnitude of the initial potential applied to the ring electrode (which determines the low mass cut-off), trap size, dimensions of apertures in the endcap electrodes and RF drive frequency. Our studies demonstrate that ion loss due to initial thermal energy increases with increase in mass and that, in the traps investigated, ion escape occurs in the radial direction. Reduction in the loss of high mass ions is favoured by lower ion temperatures, increasing low mass cut-off, increasing trap size, and higher RF drive frequencies. However, dimensions of the apertures in the endcap electrodes do not influence ion loss in the range of aperture sizes considered. (C) 2010 Elsevier B.V. All rights reserved.

Interactions of Antithyroid Drugs and Their Analogues with Halogens and their Biological Implications

The selenium analogue of antithyroid drug methimazole (MSeI) reacts with molecular bromine to produce two different types of novel complexes depending upon the molar ratio of MSeI to Br-2 in the reaction medium: Dicationic diselenide complex with two Br- ions as counterions is produced in the reaction of MSeI with 0.5 equiv of Br-2 (MSeI/Br-2, 1.0:0.5), whereas a stable 10-Se-3 hypervalent ``T-shaped'' complex featuring a linear Br-Se-Br moiety was produced when MSeI was treated with Br-2 in an equimolar ratio (MSeI/Br-2, 1.0:1.0). A substitution at the free N-H group in MSeI alters its reactivity toward iodine/bromine. For example, the N,N-disubstituted selones exclusively produce the corresponding 10-Se-3 hypervalent ``T-shaped'' complexes in the reaction with I-2. In the presence of the lectoperoxidase/H2O2/I- system, N,N-dimethylimidazole-2-selone produces the corresponding dicationic diselenide with two I- counterions as the final metabolite. The formation of ionic species in these reactions is confirmed by single crystal X-ray diffraction studies and in some cases by Fourier transform-Raman spectroscopic investigations.

Temperature dependence of the levitation effect - Implications for separation of multicomponent mixtures

Sufficiently long molecular dynamics simulations have been carried out on spherical monatomic sorbates in NaY zeolite, interacting via simple Lennard-Jones potentials, to investigate the dependence of the levitation effect on the temperature. Simulations carried out in the range 100-300 K suggest that the anomalous peak in the diffusion coefficient (observed when the levitation parameter, gamma, is near unity) decreases in intensity with increase in temperature. The rate of cage-to-cage migrations also exhibits a similar trend. The activation energy obtained from Arrhenius plots is found to exhibit a minimum when the diffusion coefficient is a maximum, corresponding to the gamma approximate to 1 sorbate diameter. In the linear or normal regime, the activation energy increases with increase in sorbate diameter until it shows a sharp decrease in the anomalous regime. Locations and energies of the adsorption sites and their dependence on the sorbate size gives interesting insight into the nature of the underlying potential-energy surface and further explain the observed trend in the activation energy with sorbate size. Cage residence times, tau(c), show little or no change with temperature for the sorbate with diameter corresponding to gamma approximate to 1, whereas there is a significant decrease in tau(c) with increase in temperature for sorbates in the linear regime. The implications of the present study for the separation of mixtures of sorbates are discussed.

Statistical thermodynamics of lattice models in zeolites: Implications of local versus global mean field interactions

The statistical thermodynamics of adsorption in caged zeolites is developed by treating the zeolite as an ensemble of M identical cages or subsystems. Within each cage adsorption is assumed to occur onto a lattice of n identical sites. Expressions for the average occupancy per cage are obtained by minimizing the Helmholtz free energy in the canonical ensemble subject to the constraints of constant M and constant number of adsorbates N. Adsorbate-adsorbate interactions in the Brag-Williams or mean field approximation are treated in two ways. The local mean field approximation (LMFA) is based on the local cage occupancy and the global mean field approximation (GMFA) is based on the average coverage of the ensemble. The GMFA is shown to be equivalent in formulation to treating the zeolite as a collection of interacting single site subsystems. In contrast, the treatment in the LMFA retains the description of the zeolite as an ensemble of identical cages, whose thermodynamic properties are conveniently derived in the grand canonical ensemble. For a z coordinated lattice within the zeolite cage, with epsilon(aa) as the adsorbate-adsorbate interaction parameter, the comparisons for different values of epsilon(aa)(*)=epsilon(aa)z/2kT, and number of sites per cage, n, illustrate that for -1 0. We compare the isotherms predicted with the LMFA with previous GMFA predictions [K. G. Ayappa, C. R. Kamala, and T. A. Abinandanan, J. Chem. Phys. 110, 8714 (1999)] (which incorporates both the site volume reduction and a coverage-dependent epsilon(aa)) for xenon and methane in zeolite NaA. In all cases the predicted isotherms are very similar, with the exception of a small steplike feature present in the LMFA for xenon at higher coverages. (C) 1999 American Institute of Physics. [S0021-9606(99)70333-8].

Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution

In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced, The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications. (C) 1999 Elsevier Science B.V. All rights reserved.

Implications of the half-duplex constraint on relay-aided cooperation using rateless codes

The half-duplex constraint, which mandates that a cooperative relay cannot transmit and receive simultaneously, considerably simplifies the demands made on the hardware and signal processing capabilities of a relay. However, the very inability of a relay to transmit and receive simultaneously leads to a potential under-utilization of time and bandwidth resources available to the system. We analyze the impact of the half-duplex constraint on the throughput of a cooperative relay system that uses rateless codes to harness spatial diversity and efficiently transmit information from a source to a destination. We derive closed-form expressions for the throughput of the system, and show that as the number of relays increases, the throughput approaches that of a system that uses more sophisticated full-duplex nodes. Thus, half-duplex nodes are well suited for cooperation using rateless codes despite the simplicity of both the cooperation protocol and the relays.

Insights into the Regulatory Characteristics of the Mycobacterial Dephosphocoenzyme A Kinase: Implications for the Universal CoA Biosynthesis Pathway

Being vastly different from the human counterpart, we suggest that the last enzyme of the Mycobacterium tuberculosis Coenzyme A biosynthetic pathway, dephosphocoenzyme A kinase (CoaE) could be a good anti-tubercular target. Here we describe detailed investigations into the regulatory features of the enzyme, affected via two mechanisms. Enzymatic activity is regulated by CTP which strongly binds the enzyme at a site overlapping that of the leading substrate, dephosphocoenzyme A (DCoA), thereby obscuring the binding site and limiting catalysis. The organism has evolved a second layer of regulation by employing a dynamic equilibrium between the trimeric and monomeric forms of CoaE as a means of regulating the effective concentration of active enzyme. We show that the monomer is the active form of the enzyme and the interplay between the regulator, CTP and the substrate, DCoA, affects enzymatic activity. Detailed kinetic data have been corroborated by size exclusion chromatography, dynamic light scattering, glutaraldehyde crosslinking, limited proteolysis and fluorescence investigations on the enzyme all of which corroborate the effects of the ligands on the enzyme oligomeric status and activity. Cysteine mutagenesis and the effects of reducing agents on mycobacterial CoaE oligomerization further validate that the latter is not cysteine-mediated or reduction-sensitive. These studies thus shed light on the novel regulatory features employed to regulate metabolite flow through the last step of a critical biosynthetic pathway by keeping the latter catalytically dormant till the need arises, the transition to the active form affected by a delicate crosstalk between an essential cellular metabolite (CTP) and the precursor to the pathway end-product (DCoA).

Prevalence of, and antigenic variation in, serotype G10 rotaviruses and detection of serotype G3 strains in diarrheic calves: Implications for the origin of G10P11 or P11 type reassortant asymptomatic strains in newborn children in India

Previous studies have shown predominant association of G10P11 type bovine rotavirus-derived reassortant strains with asymptomatic infections in newborn children in India. To understand the epidemiological and genetic basis for the origin of these strains in humans, the relative frequencies of different serotypes among bovine rotaviruses (BRVs) isolated from southern, western and central regions of the country were determined by subgroup and serotype analysis as well as nucleotide (nt) sequence analysis of the genes encoding the outer capsid proteins VP4 and VP7. Since the human G10P11 asymptomatic neonatal strain I321 possessed NSP1 from a human rotavirus, to determine its genetic origin in the bovine strains, comparative analysis of partial gene sequences from representative G10P11 strains was also carried out. The following observations were of great epidemiological significance, (i) G10P11 strains predominated in all the three regions with frequencies ranging between 55.6% and 85.2%. In contrast to the high prevalence of G6 strains in other countries, only one G6 strain was detected in this study and G8 strains represented 5.8% of the isolates, (ii) among the G10 strains, in serotyping ELISA, four patterns of reactivity were observed that appeared to correlate with the differences in electropherotypic patterns and amino acid (aa) sequence of the VP7, (iii) surprisingly, strains belonging to serotype G3 were detected more frequently (10.7%) than those of serotypes G6 and G8 combined, while strains representing the new serotype (G15) were observed in a single farm in Bangalore, and (iv) about 3.9% of the isolates were nontypeable as they exhibited high cross-reactivity to the serotyping MAbs used in the study. Comparative analysis of the VP7 gene sequence from the prototype G3 MAb-reactive bovine strain J63 revealed greatest sequence relatedness (87.6% nt and 96.0% aa) with that of serotype G3 rhesus-monkey strain RRV. It also exhibited high sequence homology with the VP7 from several animal and animal rotavirus-related human G3 strains (Simian SA11; equine ERV316 and FI-14. canine CU-1 and K9; porcine 4F; Feline Cat2 and human HCR3, YO and AU1). Partial nucleotide sequence analysis of the NSP1 gene of J63 showed greatest nt sequence homology (95.9%) to the NSP1 gene allele of the Indian G8 strain, isolated from a diarrheic child, which is likely to have been transmitted directly from cattle and 92.6% homology to that of the bovine G8 strain A5-10 suggesting the likely origin of J63 by gene reassortment between a bovine G8 strain and a G3 animal strain. Prevalence of G10P11 strains in cattle and G10P11 or P11 type reassortant strains in asymptomatic neonates as well as detection of G8P[1] strains in diarrheic children support our hypothesis for bidirectional transmission of rotaviruses between humans and cattle and origin of novel strains catalyzed by the age-old traditions and socio-economic conditions in India.

A model for tool-use traditions in primates: implications for the coevolution of culture and cognition

Inspired by the demonstration that tool-use variants among wild chimpanzees and orangutans qualify as traditions (or cultures), we developed a formal model to predict the incidence of these acquired specializations among wild primates and to examine the evolution of their underlying abilities. We assumed that the acquisition of the skill by an individual in a social unit is crucially controlled by three main factors, namely probability of innovation, probability of socially biased learning, and the prevailing social conditions (sociability, or number of potential experts at close proximity). The model reconfirms the restriction of customary tool use in wild primates to the most intelligent radiation, great apes; the greater incidence of tool use in more sociable populations of orangutans and chimpanzees; and tendencies toward tool manufacture among the most sociable monkeys. However, it also indicates that sociable gregariousness is far more likely to produce the maintenance of invented skills in a population than solitary life, where the mother is the only accessible expert. We therefore used the model to explore the evolution of the three key parameters. The most likely evolutionary scenario is that where complex skills contribute to fitness, sociability and/or the capacity for socially biased learning increase, whereas innovative abilities (i.e., intelligence) follow indirectly. We suggest that the evolution of high intelligence will often be a byproduct of selection on abilities for socially biased learning that are needed to acquire important skills, and hence that high intelligence should be most common in sociable rather than solitary organisms. Evidence for increased sociability during hominin evolution is consistent with this new hypothesis. (C) 2003 Elsevier Science Ltd. All rights reserved.

Taxonomic Implications of a Field Study of Morphotypes of Hanuman Langurs (Semnopithecus entellus) in Peninsular India

The Hanuman langur is one of the most widely distributed and morphologically variable non-human primates in South Asia. Even though it has been extensively studied, the taxonomic status of this species remains unresolved due to incongruence between various classification schemes. This incongruence, we believe, is largely due to the use of plastic morphological characters such as coat color in classification. Additionally these classification schemes were largely based on reanalysis of the same set of museum specimens. To bring greater resolution in Hanuman langur taxonomy we undertook a field survey to study variation in external morphological characters among Hanuman langurs. The primary objective of this study is to ascertain the number of morphologically recognizable units (morphotypes) of Hanuman langur in peninsular India and to compare our field observations with published classification schemes. We typed five color-independent characters for multiple adults from various populations in South India. We used the presence-absence matrix of these characters to derive the pair-wise distance between individuals and used this to construct a neighbor-joining (NJ) tree. The resulting NJ tree retrieved six distinct clusters, which we assigned to different morphotypes. These morphotypes can be identified in the field by using a combination of five diagnostic characters. We determined the approximate distributions of these morphotypes by plotting the sampling locations of each morphotype on a map using GIS software. Our field observations are largely concordant with some of the earliest classification schemes, but are incongruent with recent classification schemes. Based on these results we recommend Hill (Ceylon Journal of Science, Colombo 21:277-305, 1939) and Pocock (Primates and carnivora (in part) (pp. 97-163). London: Taylor and Francis, 1939) classification schemes for future studies on Hanuman langurs.