Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn²⁺ finger motifs in the CTD. The Zn²⁺ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn²⁺ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn²⁺ fingers from the mycobacterial topoI could be associated with Zn²⁺ export and homeostasis.     

The effect of Meloidogyne incognita on the histopathology of Momordica charantia roots

Bitter gourd (Momordica charantia L.) was inoculated with root-knot nematode Meloidogyne incognita to investigate the anatomical abnormalities in the affected roots. Soon after inoculation the second-stage juveniles (J2) entered at or near the root caps and migrated intercellularly towards the zone of vascular differentiation. Discrete giant cells were observed after three days of inoculation. The nematode induced hypertrophy and hyperplasia near the giant cells. After six days, the juveniles moulted to their third stage (J3). At the same, time giant cell size and density of giant cell cytoplasm increased. The continuity of vascular strands remained unaffected. Between 12 and 24 days of inoculation the giant cells enlarged several times and became multinucleate and enclosed dense and granular cytoplasm. The nematodes became almost pyriform 18 days after inoculation. The orientation of vascular strands changed, due to hypertrophy, hyperplasia and enlargement of the nematode. After 30 days of inoculation the nematodes developed into mature females and started egg laying. A large amount of parenchyma transformed into abnormal xylem.     

A survey of die-back disease of neem in Tamil Nadu,India and PCR-based confirmation of the isolates

A survey of die-back disease of neem was done in different agro climatic regions of Tamil Nadu, India using Global Positioning System (GARMIN 12). Twigs of Azadirachta indica (Neem) infected with die-back were collected from different regions of Tamil Nadu, India and they were further analyzed to determine the pathogen. Phomopsis azadirachtae the causal organism was isolated on malt extract agar from die-back infected neem twigs. They were identified by conventional and molecular methods. Phomopsis genus specific primers (5.8S r-DNA) were then used for the confirmation of P. azadirachtae – the causative agent of die-back of neem by Polymerase chain reaction (PCR). Studies revealed the amplification of expected 141bp DNA in P. azadirachtae isolated from the diseased trees of different regions of Tamil Nadu confirming the causal organism of die-back of neem. Studies revealed a very high incidence of die-back in most of the places of Tamil Nadu. Hand held GPS was used in the study which would help in continuous monitoring of the diseased trees.     

Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1

Cellular protein synthesis is initiated with methionine in eukaryotes with few exceptions. Methionine aminopeptidases (MetAPs) which catalyze the process of N-terminal methionine excision are essential for all organisms. In mammals, type 2 MetAP (MetAP2) is known to be important for angiogenesis, while type 1 MetAP (MetAP1) has been shown to play a pivotal role in cell proliferation. Our previous high-throughput screening of a commercial compound library uncovered a novel class of inhibitors for both human MetAP1 (HsMetAP1) and human MetAP2 (HsMetAP2). This class of inhibitors contains a pyridinylpyrimidine core. To understand the structure–activity relationship (SAR) and to search for analogues of 2 with greater potency and higher HsMetAP1-selectivity, a total of 58 analogues were acquired through either commercial source or by in-house synthesis and their inhibitory activities against HsMetAP1 and HsMetAP2 were determined. Through this systematic medicinal chemistry analysis, we have identified (1) 5-chloro-6-methyl-2-pyridin-2-ylpyrimidine as the minimum element for the inhibition of HsMetAP1; (2) 5′-chloro as the favored substituent on the pyridine ring for the enhanced potency against HsMetAP1; and (3) long C4 side chains as the essentials for higher HsMetAP1-selectivity. At the end of our SAR campaign, 25b, 25c, 26d and 30a–30c are among the most selective and potent inhibitors of purified HsMetAP1 reported to date. In addition, we also performed crystallographic analysis of one representative inhibitor (26d) in complex with N-terminally truncated HsMetAP1.     

Two silicone nontoxic fouling release coatings: Hydrosilation cured PDMS and CaCO3 filled,ethoxysiloxane cured RTV11

Two silicone coatings have been evaluated for barnacle adhesion. One coating is an unfilled hydrosilation cured polydimethylsiloxane (PDMS) network, while the other is a room temperature vulcanized (RTV), filled, ethoxysiloxane cured PDMS elastomer, RTV11^?. The adhesion strength of one species of barnacle, Balanus eburneus, to the hydrosilation coatings is in the range of 0.37–0.60 kg cm^‐2 while the corresponding range for RTV11 is 0.64–0.90 kg cm^‐2. The easier release of B. eburneus from the hydrosilation cured network compared to RTV11 is discussed in relationship to differences in bulk and surface properties. Preliminary results suggest bulk modulus may be the most important parameter in determining barnacle adhesion strength. In light or mechanical property analysis, a re‐evaluation of surface properties and chemical stability is presented.     

Somatic embryogenesis and plant regeneration in <Emphasis Type="Italic">Catharanthus roseus</Emphasis>

Embryogenic callus in Catharanthus roseus was initiated from hypocotyl on Murashige and Skoog’s (MS) medium supplemented with 1.0–2.0 mg dm⁻³ of 2,4-dichlorophenoxyacetic acid (2,4-D) or chlorophenoxyacetic acid (CPA). Calli from other sources were non-embryogenic. Numerous somatic embryos were induced from primary callus on MS medium suplemented with naphthalene acetic acid (NAA) within two weeks of culture. Embryo proliferation was much faster on medium supplemented with 6-benzylaminopurine (BAP). After transfer to medium with gibberellic acid (GA₃, 1.0 mg dm^{− 3}) mature green embryos were developed and germinated well into plantlets on MS liquid medium supplemented with 0.5 mg dm⁻³ BAP. Later, embryos with cotyledonary leaves were subjected to different auxins treatments for the development of roots. Before transfer ex vitro, plantlets were cultivated on half strength MS medium containing 3 % sucrose and 0.5 mg dm⁻³ BAP for additional 2 weeks. Additionally, the effect of liquid medium has been evaluated at different morphogenetic stages.     

Diffusion of phosphate to plant roots in soil

Summary A method is described for computing the theoretical distribution of solutes around a root with root hairs. The P concentration profile around the primary root of a rape seedling with root hairs, growing in a low-P soil, showed considerably greater depletions than predicted by this method, using the relationship between P in soil and in solution obtained from a desorption isotherm experiment. This suggests an enhanced release of soil P into solution in the rhizosphere.Soil Science Laboratory, Department of Agricultural Science, University of Oxford     

Role of Pectinolytic Yeasts in the Degradation of Mucilage Layer of Coffea robusta Cherries

Pectinolytic yeasts, Saccharomyces marxianus, S. bayanus, S. cerevisiae var. ellipsoideus, and Schizosaccharomyces sp., predominated in the natural fermentation of coffee cherries of Coffea robusta variety grown in Chikmagalur district of Mysore State, India. These yeast species were found on the cherry surfaces, and evidence was adduced to show that the natural fermentation of coffee was the result of activity of microflora from the cherry surface itself rather than that of flora of air or water. Incorporation of pure cultures of Saccharomyces species was shown to aid the process when a mixture of all three species was used. An enzyme preparation from the Saccharomyces species was observed to hasten the mucilage-layer degradation.     

Isolation and properties of catechol-cleaving yeasts from coir rets

A suitable method for the selective isolation of catechol-cleaving yeasts from coir rets has been worked out. The yeast strains, all belonging toDebaryomyces hansenii, were found to demand biotin as an essential vitamin. The organism has the ability to grow on catechol, phenol and some related compounds as sole source of carbon. It tolerates 0.4% catechol and 0.26% phenol. Evidence was obtained that the catechol-cleaving enzyme of the isolates is a pyrocatechase. Some properties of the cell-free catechol oxygenase are described.     

Effect of root exudates and extracts on rhizosphere fungi

Summary The effects of root exudates and extracts of Cassia tora L. and Crotalaria medicaginea Lamk., on some dominant rhizosphere fungi isolated from the plants were studied. Root extracts induced a high degree of stimulation in rate of growth of a majority of the fungi tested. Root exudates caused only a marginal effect which was positive on all the fungi except Trichoderma lignorum which was inhibited by the root exudate of C. medicaginea.