Characterization of the DNA-binding domain and identification of the active site residue in the ‘Gyr A’ half of Leishmania donovani topoisomerase II

DNA topoisomerase II is a multidomain homodimeric enzyme that changes DNA topology by coupling ATP hydrolysis to the transport of one DNA helix through a transient double-stranded break in another. To investigate the biochemical properties of the individual domains of Leishmania donovani topoisomerase II, four truncation mutants were generated. Deletion of 178 aminoacids from the C-terminus (core and LdΔC1058) had no apparent effect on the DNA-binding or cleavage activities of the enzymes. However, when 429 aminoacids from the N-terminus and 451 aminoacids from the C-terminus were removed (LdΔNΔC), the enzyme was no longer active. Moreover, the removal of 429 aminoacids from the N-terminus (LdΔNΔC, core and LdΔN429) render the mutant proteins incapable of performing ATP hydrolysis. The mutant proteins show cleavage activities at wide range of KCl concentrations (25–350 mM). In addition, the mutant proteins, excepting LdΔNΔC, can also act on kDNA and linearize the minicircles. Surprisingly, the mutant proteins fail to show the formation of the enhanced cleavable complex in the presence of etoposide. Our findings suggest that the conformation required for interaction with the drug is absent in the mutant proteins. Here, we have also identified Tyr(775) through direct sequencing of the DNA linked peptide as the catalytic residue implicated in DNA-breakage and rejoining. Taken together, our results demonstrate that topoisomerase II are functionally and mechanistically conserved enzymes and the variations in activity seem to reflect functional optimization for its physiological role during parasite genome replication

P4P_4-free Partition and Cover Numbers and Application

$P_4$-free graphs-- also known as cographs, complement-reducible graphs, or hereditary Dacey graphs--have been well studied in graph theory. Motivated by computer science and information theory applications, our work encodes (flat) joint probability distributions and Boolean functions as bipartite graphs and studies bipartite $P_4$-free graphs. For these applications, the graph properties of edge partitioning and covering a bipartite graph using the minimum number of these graphs are particularly relevant. Previously, such graph properties have appeared in leakage-resilient cryptography and (variants of) coloring problems. Interestingly, our covering problem is closely related to the well-studied problem of product/Prague dimension of loopless undirected graphs, which allows us to employ algebraic lower-bounding techniques for the product/Prague dimension. We prove that computing these numbers is \npol-complete, even for bipartite graphs. We establish a connection to the (unsolved) Zarankiewicz problem to show that there are bipartite graphs with size-$N$ partite sets such that these numbers are at least ${\epsilon\cdot N^{1-2\epsilon}}$, for $\epsilon\in\{1/3,1/4,1/5,\dotsc\}$. Finally, we accurately estimate these numbers for bipartite graphs encoding well-studied Boolean functions from circuit complexity, such as set intersection, set disjointness, and inequality. For applications in information theory and communication \& cryptographic complexity, we consider a system where a setup samples from a (flat) joint distribution and gives the participants, Alice and Bob, their portion from this joint sample. Alice and Bob\u27s objective is to non-interactively establish a shared key and extract the left-over entropy from their portion of the samples as independent private randomness. A genie, who observes the joint sample, provides appropriate assistance to help Alice and Bob with their objective. Lower bounds to the minimum size of the genie\u27s assistance translate into communication and cryptographic lower bounds. We show that (the $\log_2$ of) the $P_4$-free partition number of a graph encoding the joint distribution that the setup uses is equivalent to the size of the genie\u27s assistance. Consequently, the joint distributions corresponding to the bipartite graphs constructed above with high $P_4$-free partition numbers correspond to joint distributions requiring more assistance from the genie. As a representative application in non-deterministic communication complexity, we study the communication complexity of nondeterministic protocols augmented by access to the equality oracle at the output. We show that (the $\log_2$ of) the $P_4$-free cover number of the bipartite graph encoding a Boolean function $f$ is equivalent to the minimum size of the nondeterministic input required by the parties (referred to as the communication complexity of $f$ in this model). Consequently, the functions corresponding to the bipartite graphs with high $P_4$-free cover numbers have high communication complexity. Furthermore, there are functions with communication complexity close to the \naive protocol where the nondeterministic input reveals a party\u27s input. Finally, the access to the equality oracle reduces the communication complexity of computing set disjointness by a constant factor in contrast to the model where parties do not have access to the equality oracle. To compute the inequality function, we show an exponential reduction in the communication complexity, and this bound is optimal. On the other hand, access to the equality oracle is (nearly) useless for computing set intersection

Cricket performance management: mathematical formulation and analytics

This book focuses on the application of data mining techniques in cricket. It provides detailed examples of how data mining can be helpful for decision-making in sports with special reference to cricket, particularly the quantitative features related to Twenty20 cricket, the latest and the most popular format of the game. The book highlights the performance quantification of cricketers (batsmen, bowlers, all-rounders, and wicket keepers), determining the market valuation of cricketers based on their on-field performances and the effect of age on the performance of the cricketers. It also provides a comprehensive overview of the different aspects of the game where quantitative techniques are beneficial, and highlights the use of statistical and data mining tools in analysing sports-related data and objective decision-making in sports. The book appeals to a wide readership, including postgraduate students of statistics/mathematics, data analysts, sports management bodies. It also offers data miners, such as researchers in statistics, mathematics, operations research, and computer science ideas for projects

Novel Betulin Derivatives as Antileishmanial Agents with Mode of Action Targeting Type

M. Unlike CPT, these compounds do not stabilize the cleavage complex, rather they abrogate the covalent complex formation. In processive mode of relaxation assay condition, these compounds slow down the strand rotation event, which ultimately affect the relaxation of supercoiled DNA. Interestingly, these compounds reduce the intracellular parasite burden in macrophages infected with wild type Leishmania as well as with sodium antimony gluconate resistant parasite (GE1). Taken together, our data suggest that these betulin derivatives can be exploited as potential drug candidates against threatening drug resistant leishmaniasis. MOL #72785 5 Introduction

Measuring performance of batting partners in limited overs cricket

Batting and bowling are prime skills in the game of cricket. Unlike bowling, batting takes place between a pair of two batsmen, often referred to as a partnership. If a batsman is dismissed, the pair is broken and a new partnership is formed with the next batsman. However, the different existing measures of batting performance are based on individual performances and not on the basis of partnerships. This research attempts to develop a measure to quantify the batting performance of partnerships. This unique measure takes into account not only the runs scored by the partnership, but also the match situation in which the runs are scored by the batting partners. To quantify the model, the 2016 Twenty20 World Cup played in India is considered. If the partnership scores are computed for a series of matches of a given team, then the coach can identify the partnerships that bat well under pressure. It will be helpful in determining the batting order of the team so that reasonably well played partnerships under pressure shall occur more frequently in the upcoming matches. This measure can also determine the best opening batting partners for a given team in limited overs cricket.Keywords: Batting; Cricket analytics; Limited overs; Performance measurement

Biochemical assessment of extract from <em>Oxalis corniculata</em> L.: Its role in food preservation, antimicrobial and antioxidative paradigms using <em>in situ</em> and <em>in vitro</em> models

230-243Food poisoning, often due to microbial contamination and improper storage practice, is a matter of concern. Plants and plant based products are gaining interest in processed food in food industry as an alternative to synthetic antimicrobials. In this context, here, we analysed flavonoid rich methanolic extract from the creeping woodsorrel, Oxalis corniculata L. leaf for its biochemical assessments along with its bioactivity against some common pathogenic bacteria. The bioactivity of the extract as evaluated in both in vitro and in situ methods, verified that the Oxalis corniculata leafextract exert reduces power, hydroxyl radical scavenging activity, inhibition in liposome peroxidation, and DPPH free radical quenching activity. The extract also inhibited the formation of peroxide during subsequent storage in the oil-emulsion system as well as in heated oil. The greater reducing activity of the extract prevented hydroxyl radical induced pUC18 DNA strand breaks and there by retain its original conformation. The extract also prevented the oxidative damage of goat liver cells during Fenton reaction. In vitro antimicrobial experiments implied that extract has inhibitory effect against Staphylococcus aureus, Escherichia coli, Salmonella Typhi, S. Typhiimurium and Vibrio cholera. E. coli showed the highest and V. cholera the lowest sensitivities against the extract. Moreover, the extract can be utilized for preservation of fish meat as it prevented the growth of food poisoning bacteria S. aureus during storage at 10°C. HPLC chromatogram detected the predominance of three active principal components, i.e. flavonoids in the following order: rutin>p-hydroxybenzoic acid>ferulic acid

Functional dissection of the C-terminal domain of type II DNA topoisomerase from the kinetoplastid hemoflagellate Leishmania donovani

The amino acid sequences of the C-terminal domain (CTD) of the type II DNA topoisomerases are divergent and species specific as compared with the highly conserved N-terminal and central domains. A set of C-terminal deletion mutants of Leishmania donovani topoisomerase II was constructed. Removal of more than 178 amino acids out of 1236 amino acid residues from the C-terminus inactivates the enzyme, whereas removal of 118 amino acids or less has no apparent effect on the ability of the parasite enzyme to complement a temperature-sensitive mutation of the Saccharomyces cerevisiae topoisomerase II gene. Deletion analysis revealed a potent nuclear localization signal (NLS) within the amino acid residues 998–1058. Immunomicroscopy results suggest that the removal of an NLS in the CTD is likely to contribute to the physiological dysfunction of these proteins. Modeling of the LdTOP2 based on the crystal structure of the yeast type II DNA topoisomerase showed that the parasite protein assumes a structure similar to its yeast counterpart harboring all the conserved residues in a structurally similar position. However, a marked difference in electrostatic potential was found in a span of 60 amino acid residues (998–1058), which also do not have any homology with topoisomerase II sequences. Such significant differences can be exploited by the structure-based design of selective inhibitors using the structure of the Leishmania enzyme as a template

Characterization of the ATPase activity of topoisomerase II from Leishmania donovani and identification of residues conferring resistance to etoposide

We have cloned and expressed the 43 kDa N-terminal domain of Leishmania donovani topoisomerase II. This protein has an intrinsic ATPase activity and obeys Michaelis–Menten kinetics. Cross-linking studies indicate that the N-terminal domain exists as a dimer both in the presence and absence of nucleotides. Etoposide, an effective antitumour drug, traps eukaryotic DNA topoisomerase II in a covalent complex with DNA. In the present study, we report for the first time that etoposide inhibits the ATPase activity of the recombinant N-terminal domain of L. donovani topoisomerase II. We have modelled the structure of this 43 kDa protein and performed molecular docking analysis with the drug. Mutagenesis of critical amino acids in the vicinity of the ligand-binding pocket reveals less efficient inhibition of the ATPase activity of the enzyme by etoposide. Taken together, these results provide an insight for the development of newer therapeutic agents with specific selectivity