Uracil excision repair in Mycobacterium tuberculosis cell-free extracts

Uracil excision repair is ubiquitous in all domains of life and initiated by uracil DNA glycosylases (UDGs) which excise the promutagenic base, uracil, from DNA to leave behind an abasic site (AP-site). Repair of the resulting AP-sites requires an AP-endonuclease, a DNA polymerase, and a DNA ligase whose combined activities result in either short-patch or long-patch repair. Mycobacterium tuberculosis, the causative agent of tuberculosis, has an increased risk of accumulating uracils because of its G + C-rich genome, and its niche inside host macrophages where it is exposed to reactive nitrogen and oxygen species, two major causes of cytosine deamination (to uracil) in DNA. In vitro assays to study DNA repair in this important human pathogen are limited. To study uracil excision repair in mycobacteria, we have established assay conditions using cell-free extracts of M. tuberculosis and M. smegmatis (a fast-growing mycobacterium) and oligomer or plasmid DNA substrates. We show that in mycobacteria, uracil excision repair is completed primarily via long-patch repair. In addition, we show that M. tuberculosis UdgB, a newly characterized family 5 UDG, substitutes for the highly conserved family 1 UDG, Ung, thereby suggesting that UdgB might function as backup enzyme for uracil excision repair in mycobacteria. (C) 2011 Elsevier Ltd. All rights reserved.

Mutagenic significance of proton acidities in methylated guanine and thymine bases and deoxynucleosides: A theoretical study

Proton changes have been advanced as being the key molecular basis for the mutagenecity of alkylated DNA bases and nucleosides, leading to questions as to which protons are involved and whether the protic changes are tautomeric shifts or abstractions. This semiempirical molecular orbital study seeks to clarify the issue by examining the various possibilities open for these protic changes in a number of methylated guanines and thymines and their deoxynucleosides. Proton shifts leading to tautomer formation are not predicted as being thermodynamically favourable in most cases. The most feasible proton abstractions are predicted to involve the Watson-Crick protons in all cases, which corroborates Watson-Crick proton loss as providing the key molecular basis for the induction of point mutations. The calculated proton acidities correlate well with experimental data. The gas-phase deprotonation enthalpies for a number of alkylated nucleosides are found to correlate linearly with the solvent-phase pK(a) values. The theoretically calculated enthalpies in a simulated aqueous solvent phase of the deprotonation reactions of various nucleic acid bases are also found to have good linear correlations with experimental pK(a) values. The consensus of these calculations is that O-6-alkyldeoxyguanosines, and O-2- and O-4-alkyldeoxythymidines would be mutagenic while N-7-alkyldeoxyguanosines would not be mutagenic (as experiment indicates). The untested N-3-methyldeoxyguanosine is predicted to be mutagenic. (C) 1997 Elsevier Science B.V.

A Change in the 3(10)- to alpha-Helical Transition Point in the Heptapeptides Containing Sulfur and Selenium

Crystal structures of three heptapeptides Boc-Ala-Leu-Aib-XXX-Ala-Leu-Aib-OMe (where XXX = methionine in peptide A, selenomethionine in peptide B, and S-benzyl cysteine in peptide C) reveal mixed 3(10)-/alpha-helical conformations with R factors of 6.94, 5.79, and 5.98, respectively. All the structures were solved in the P2(1)2(1)2(1) space group. 3(10)- to a-helical transitions are observed in all of these peptides. The helices begin as a 3(10)-helical segment at the N-terminus and then transit for peptides A and C at residue Aib(3) carbonyl (O(3)), while for peptide B the transition occurs at residue Leu(2) carbonyl oxygen (O(2)). There are water molecules associated in the crystal of each of these peptides and they form different types of hydrogen bonding patterns in each crystal. The observations suggest that 3(10)- to alpha-helical transition is sequence dependent in these short heptapeptide sequences.

Prediction of reaeration rates in square, stirred tanks

Experiments were conducted on the oxygen transfer coefficient, k(L)a(20), through surface aeration in geometrically similar square tanks, with a rotor of diameter D fitted with six flat blades. An optimal geometric similarity of various linear dimensions, which produced maximum k(L)a(20) for any rotational speed of rotor N by an earlier study, was maintained. A simulation equation uniquely correlating k = k(L)a(20)(nu/g(2))(1/3) (nu and g are kinematic viscosity of water and gravitational constant, respectively), and a parameter governing the theoretical power per unit volume, X = (ND2)-D-3/(g(4/3)nu(1/3)), is developed. Such a simulation equation can be used to predict maximum k for any N in any size of such geometrically similar square tanks. An example illustrating the application of results is presented. Also, it has been established that neither the Reynolds criterion nor the Froude criterion is singularly valid to simulate either k or K = k(L)a(20)/N, simultaneously in all the sizes of tanks, even through they are geometrically similar. Occurrence of "scale effects" due to the Reynolds and the Froude laws of similitude on both k and K are also evaluated.

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 In general, the deviation between the LMFA and GMFA is greater for smaller n and less sensitive to n for epsilon(aa)(*)> 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].

Stress-strain Curves and Corresponding Structural Parameters in Mulberry and Non-mulberry Silk Fibers

Mulberry fiber (Bivoltine) and non-mulberry fiber (Tassar) were subjected to stress-strain studies and the corresponding samples were examined using wide angle X-ray scattering studies. Here we have two different characteristic stress-strain curves and this has been correlated with changes in crystallite shape ellipsoids in all the fibers. Exclusive crystal structure studies of Tassar fibers show interesting feature of transformation from antiparallel chains to parallel chains.

Total peroxidase activity and peroxidase isoforms as modified by salt stress in two cultivars of fox-tail millet with differential salt tolerance

The effect of NaCl on total peroxidase activity, induction of isoperoxidases and lipid peroxidation in 5-day-old seedlings of two contrasting genotypes of Setaria italica L. (Prasad, a salt tolerant cultivar and Lepakshi, a salt susceptible cultivar), was studied. Total peroxidase activity increased under NaCl salinity and the degree of elevation in the activity was salt concentration dependent. Nevertheless, a greater activity was recorded in the tolerant cultivar (cv Prasad) compared to the susceptible (cv Lepakshi) one in all days of sampling. Further, the pattern of isoperoxidases was modified during stress conditions as evident from the electrophoregrams. Although, five acidic isoforms were detected in both cultivars, differences were found between the cultivars. Furthermore, it was observed that acidic isoperoxidases were strongly expressed and an acidic isoperoxidase, A(3p) (27 kDa) is specifically found in the tolerant cultivar (cv Prasad) under NaCl stress. This isoform was partially purified and found to be thermostable with pr 5.5 and the optimum pH 7.4. A close correlation exists between the rate of lipid peroxidation in terms of malonaldehyde (MDA) content and total peroxidase activity per gram fresh weight with salt tolerance of the two cultivars. The tolerant cultivar (cv Prasad) had low MDA content and high total peroxidase activity than the susceptible variety (cv Lepakshi) during salinity stress. (C) 1999 Published by Elsevier Science Ireland Ltd. All rights reserved.

A C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins

The serendipitous observation of a C-H...O hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C-H...O interaction between the T - 4 (CH)-H-alpha and T + 1 C=O group (C...O 3.5 Angstrom) becomes possible only when the T + 1 residue adopts an extended beta conformation (T is defined as the helix terminating residue adopting an alpha(L) conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational. preferences at positions T - 4, T, and T + 1 determined. A marked preference for residues like Set, Glu and Gln is observed at T - 4 position with the motif being further stabilized by the formation of a side-chain-backbone O...H-N hydrogen bond involving the side-chain of residue T - 4 and the N-H group of residue T + 3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in beta conformation. In a majority of these cases, the succeeding beta strand lies approximately antiparallel with the helix, suggesting that the backbone C-H...O interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C-H...O hydrogen bonds between (T - 4) (CH)-H-alpha...C=O (T + 1) and (T - 8) (CH)-H-alpha...C=O (T + 3). 0 2002 Published by Elsevier Science Ltd.

A comparative analysis of regeneration in natural forests and joint forest management plantations in Uttara Kannada district, Western Ghats

Five villages undertaking joint forest management (JFM) were chosen in Uttara Kannada district, Karnataka for assessing regeneration in plantations and nearby natural forests of the village. Species number, stem density, diversity index, similarity in species composition in less disturbed and disturbed forests and plantations in the village were compared. Stem density was low in all the disturbed forests; however, the species number was low in disturbed forests of three villages and high in two villages. Plantations showed lower diversity values compared to the adjacent natural forests. Regeneration in all less disturbed forests was better compared to the disturbed counterparts. Villages were ranked based on number of landless families, per, capita forest available and number of cut stems. Assessment of village forests using ranks indicates that parameters such as per capita availability, cut stems in the forests may determine the success of JFM.

Cross-taxon surrogacy of biodiversity in the Indian Garhwal Himalaya

Biodiversity surveys were conducted in 13, 10x50 m(2) plots located between 1400 to 3100 in abode mean sea level in a range of habitats in temperate mixed Oak and Coniferous forests through sub-alpine to the alpine grasslands in Chamoli district of Uttaranchal state in the Indian Garhwal Himalaya. Cross-taxon congruence in biodiversity (alpha-diversity and beta-diversity) across macrolichens, mosses, liverworts, woody plants (shrubs and trees) and ants was investigated, so as to examine the extent to which these group, of organisms can function as Surrogates for each other. Although woody plants provided a major substrate for macrolichens and mosses, there was no species-specific association between them. Woody plant species richness was highly positively correlated with mosses (r(2) = 0.63, P < 0.001) but the relationship, as not particularly very strong with lichens and liverworts. While there was a significant correlation in the species turnover (β-diversity) of macrolichens with mosses (r(2) = 0.21 P < 0.005). the relationship was relatively poor with the woody plants. On the other hand. negative correlations emerged in the species richness of ants with those of macrolichens, mosses and woody plants (r(2) = -0.44 P < 0.05). but most of the complementarity (turnover) relationships among them were positive, Since diversity between taxonomic hierarchies within the group was consistently significantly positively correlated in all these taxa, the higher taxonomic categories Such as genus and family may be employed as surrogates for rapid assessment and monitoring of species diversity, Although no single group other than macrolichens has emerged as a good indicator of changes in species richness in all other groups, some concordant relationships between them conform to the hypothesis that species assemblages of certain taxonomic groups could still be used as surrogates for efficient monitoring of species diversity in other groups whose distribution may further predict the importance of conserving overall biodiversity in landscapes such as the Garhwal Himalaya. (C) 2002 Elsevier Science Ltd. All rights reserved.

Morphology and thermal characteristics of nano-sized Pb-Sn inclusions in Al

Nanoembedded aluminum alloys with bimetallic dispersoids of Sn and Pb of compositions Sn-82-Pb-18,Pb- Sn-64-Pb-36, and Sn-54-Pb-46 were synthesized by rapid solidification. The two phases, face-centered-cubic Pb and tetragonal Sn solid-solution, coexist in all the particles. The crystallographic relation between the two phases and the matrix depends upon the solidification pathways adopted by the particles. For Al-(Sn-82-Pb-18), we report a new orientation relation given by [011]Al//[010]Sn and (011)Al//(101)Sn. Pb exhibits a cube-on-cube orientation with Al in few particles, while in others no orientation relationship could be observed. In contrast, Pb in Sn-64-Pb-36 and Sn-54-Pb-46 particles always exhibits cube-on-cube orientation with the matrix. Sn does not show any orientation relationship with Al or Pb in these cases. Differential scanning calorimetry studies revealed melting at eutectic temperature for all compositions, although solidification pathways are different. Attempts were made to correlate these with the melting and heterogeneous nucleation. characteristics.

On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Phase transformation and semiconductor-metal transition in thin films of VO2 deposited by low-pressure metalorganic chemical vapor deposition

Thin films of the semiconducting, monoclinic vanadium dioxide, VO2(M) have been prepared on ordinary glass by two methods: directly by low-pressure metalorganic chemical vapor deposition (MOCVD), and by argon-annealing films of the VO2(B) phase deposited by MOCVD. The composition and microstructure of the films have been examined by x-ray diffraction, scanning electron microscopy, and transmission electron microscopy. Films made predominantly of either the B or the M phase, as deposited, can only be obtained over a narrow range of deposition temperatures. At the lower end of this temperature range, the as-deposited films are strongly oriented, although the substrate is glass. This can be understood from the drive to minimize surface energy. Films of the B phase have a platelet morphology, which leads to an unusual microstructure at the lower-deposition temperatures. Those grown at similar to370 degreesC convert to the metallic, rutile (R) phase when annealed at 550 degreesC, whereas those deposited at 420 degreesC transform to the R phase only at 580 degreesC. (When cooled to room temperature, the annealed films convert reversibly from the R phase to the M phase.) Electron microscopy shows that annealing leads to disintegration of the single crystalline VO2(B) platelets into small crystallites of VO2(R), although the platelet morphology is retained. When the annealing temperature is relatively low, these crystallites are nanometer sized. At a higher-annealing temperature, the transformation leads to well-connected and similarly oriented large grains of VO2(R), enveloped in the original platelet. The semiconductor-metal transition near 68 degreesC leads to a large jump in resistivity in all the VO2(M) films, nearly as large as in epitaxial films on single-crystal substrates. When the annealed films contain well-connected large grains, the transition is very sharp. Even when preferred orientation is present, the transition is not as sharp in as-deposited VO2(M), because the crystallites are not densely packed as in annealed VO2(B). However, the high degree of orientation in these films leads to a narrow temperature hysteresis. (C) 2002 American Institute of Physics.

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.

Symmetry-breaking transitions in equilibrium shapes of coherent precipitates: Effect of elastic anisotropy and inhomogeneity

We examine the symmetry-breaking transitions in equilibrium shapes of coherent precipitates in two-dimensional (2-D) systems under a plane-strain condition with the principal misfit strain components epsilon(xx)*. and epsilon(yy)*. For systems with cubic elastic moduli, we first show all the shape transitions associated with different values of t = epsilon(yy)*/epsilon(xx)*. We also characterize each of these transitions, by studying its dependence on elastic anisotropy and inhomogeneity. For systems with dilatational misfit (t = 1) and those with pure shear misfit (t = -1), the transition is from an equiaxed shape to an elongated shape, resulting in a break in rotational symmetry. For systems with nondilatational misfit (-1 < t < 1; t not equal 0), the transition involves a break in mirror symmetries normal to the x- and y-axes. The transition is continuous in all cases, except when 0 < t < 1. For systems which allow an invariant line (-1 less than or equal to t < 0), the critical size increases with an increase in the particle stiffness. However, for systems which do not allow an invariant line (0 < t less than or equal to 1), the critical size first decreases, reaches a minimum, and then starts increasing with increasing particle stiffness; moreover, the transition is also forbidden when the particle stiffness is greater than a critical value.