Working group report: Quantum chromodynamics sub-group

This is the report of the QCD working sub-group at the Tenth Workshop on High Energy Physics Phenomenology (WHEPP-X).

Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action

The crystal structures of complexes of Mycobacterium tuberculosis pantothenate kinase with the following ligands have been determined: (i) citrate; (ii) the nonhydrolysable ATP analogue AMPPCP and pantothenate (the initiation complex); (iii) ADP and phosphopantothenate resulting from phosphorylation of pantothenate by ATP in the crystal (the end complex); (iv) ATP and ADP, each with half occupancy, resulting from a quick soak of crystals in ATP (the intermediate complex); (v) CoA; (vi) ADP prepared by soaking and cocrystallization, which turned out to have identical structures, and (vii) ADP and pantothenate. Solution studies on CoA binding and catalytic activity have also been carried out. Unlike in the case of the homologous Escherichia coli enzyme, AMPPCP and ADP occupy different, though overlapping, locations in the respective complexes; the same is true of pantothenate in the initiation complex and phosphopantothenate in the end complex. The binding site of MtPanK is substantially preformed, while that of EcPanK exhibits considerabl plasticity. The difference in the behaviour of the E. coli and M. tuberculosis enzymes could be explained in terms of changes in local structure resulting from substitutions. It is unusual for two homologous enzymes to exhibit such striking differences in action. Therefore, the results have to be treated with caution. However, the changes in the locations of ligands exhibited by M. tuberculosis pantothenate kinase are remarkable and novel.

Prop-2-ynyl as a protective group for carboxylic acids: A mild method for the highly selective deprotection of prop-2-ynyl esters using tetrathiomolybdate

It is shown that prop-2-ynyl esters are useful protecting groups for carboxylic acids and that they are selectively deprotected in the presence of other esters on treatment with tetrathiomolybdate under mild conditions.

Xylan-Degrading Enzymes from the Thermophilic Fungus Humicola Zanuginosa (Griffon and Maublanc) Bunce: Action Pattern of Xylanase and beta-Glucosidase on Xylans, Xylooligomers and Arabinoxylooligomers

The mode of action of xylanase and beta-glucosidase purified from the culture filtrate of Humicola lanuginosa (Griffon and Maublanc) Bunce on the xylan extracted from sugarcane bagasse and on two commercially available larchwood and oat spelt xylans, on xylooligomers and on arabinoxylooligomers was studied. While larchwood and oat spelt xylans were hydrolyzed to the same extent in 24 h, sugarcane bagasse xylan was hydrolyzed to a lesser extent in the same period. It was found that the rate of hydrolysis of xylooligomers by xylanase increased with increase in chain length, while beta-glucosidase acted rather slowly on all the oligomers tested. Xylanase exhibited predominant ''endo'' action on xylooligomers attacking the xylan chain at random while beta-glucosidase had ''exo'' action, releasing one xylose residue at a time. On arabinoxylooligomers, however, xylanase exhibited ''exo'' action. Thus, it appears that the presence of the arabinose substituent has, in some way, rendered the terminal xylose-xylose linkage more susceptible to xylanase action. It was also observed that even after extensive hydrolysis with both the enzymes, substantial amounts of the parent arabinoxylooligomer remained unhydrolyzed together with the accumulation of arabinoxylobiose. It can therefore be concluded that the presence of the arabinose substituent in the xylan chain results in linkages that offer resistance to both xylanase and beta-glucosidase action.

Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

A Classification of Homogeneous Operators in the Cowen-Douglas Class

A complete list of homogeneous operators in the Cowen-Douglas class B-n(D) is given. This classification is obtained from an explicit realization of all the homogeneous Hermitian holomorphic vector bundles on the unit disc under the action of the universal covering group of the bi-holomorphic automorphism group of the unit disc.

Action of Transition Metal Oxides on Composite Solid Propellants

The catalytic effects of Fe2O3, Ni2O3, MnO2, and Co2O3 transition metal oxides (TMO) on the combustion of polystyrene and carboxyl-terminated polybutadiene were investigated. The order of activity of TMO's was explained by the presence of Co and absence of Fe and Ni in their lattice systems along with a reduced electron-transfer process; in systems which induce the metal ions to enter the lattice, the electron transfer process is much greater. The thermal decomposition of ammonium perchlorate propellants was enhanced to a greater extent by Co2O3 and MnO2 than by Fe2O3 and Ni2O3.

Systematic stability analysis of the renormalization group flow for the normal-superconductor-normal junction of Luttinger liquid wires

We study the renormalization group flows of the two terminal conductance of a superconducting junction of two Luttinger liquid wires. We compute the power laws associated with the renormalization group flow around the various fixed points of this system using the generators of the SU(4) group to generate the appropriate parametrization of an matrix representing small deviations from a given fixed point matrix [obtained earlier in S. Das, S. Rao, and A. Saha, Phys. Rev. B 77, 155418 (2008)], and we then perform a comprehensive stability analysis. In particular, for the nontrivial fixed point which has intermediate values of transmission, reflection, Andreev reflection, and crossed Andreev reflection, we show that there are eleven independent directions in which the system can be perturbed, which are relevant or irrelevant, and five directions which are marginal. We obtain power laws associated with these relevant and irrelevant perturbations. Unlike the case of the two-wire charge-conserving junction, here we show that there are power laws which are nonlinear functions of V(0) and V(2kF) [where V(k) represents the Fourier transform of the interelectron interaction potential at momentum k]. We also obtain the power law dependence of linear response conductance on voltage bias or temperature around this fixed point.

Watson-Crick pairing, the Heisenberg group and Milnor invariants

We study the secondary structure of RNA determined by Watson-Crick pairing without pseudo-knots using Milnor invariants of links. We focus on the first non-trivial invariant, which we call the Heisenber invariant. The Heisenberg invariant, which is an integer, can be interpreted in terms of the Heisenberg group as well as in terms of lattice paths. We show that the Heisenberg invariant gives a lower bound on the number of unpaired bases in an RNA secondary structure. We also show that the Heisenberg invariant can predict allosteric structures for RNA. Namely, if the Heisenberg invariant is large, then there are widely separated local maxima (i.e., allosteric structures) for the number of Watson-Crick pairs found.

Paracrine action of sFLT-1 secreted by stably-transfected Ehrlich ascites tumor cells and therapy using sFLT-1 inhibits ascites tumor growth in vivo

Background Vascular endothelial growth factor (VEGF) is known to play a major role in angiogenesis. A soluble form of Flt-1, a VEGF receptor, is potentially useful as an antagonist of VEGF, and accumulating evidence suggests the applicability of sFlt-1 in tumor suppression. In the present study, we have developed and tested strategies targeted specifically to VEGF for the treatment of ascites formation.Methods As an initial strategy, we produced recombinant sFLT-1 in the baculovirus expression system and used it as a trap to sequester VEGF in the murine ascites carcinoma model. The effect of the treatment on the weight of the animal, cell number, ascites volume and proliferating endothelial cells was studied. The second strategy involved, producing Ehrlich ascites tumor (EAT) cells stably transfected with vectors carrying cDNA encoding truncated form of Flt-1 and using these cells to inhibit ascites tumors in a nude mouse model. Results The sFLT-1 produced by the baculovirus system showed potent antiangiogenic activity as assessed by rat cornea and tube formation assay. sFLT-1 treatment resulted in reduced peritoneal angiogenesis with a concomitant decrease in tumor cell number, volume of ascites, amount of free VEGF and the number of invasive tumor cells as assayed by CD31 staining. EAT cells stably transfected with truncated form of Flt-1 also effectively reduced the tumor burden in nude mice transplanted with these cells, and demonstrated a reduction in ascites formation and peritoneal angiogenesis. Conclusions The inhibition of peritoneal angiogenesis and tumor growth by sequestering VEGF with either sFlt-1 gene expression by recombinant EAT cells or by direct sFLT-1 protein therapy is shown to comprise a potential therapy. Copyright (C) 2009 John Wiley & Sons, Ltd.

Comment on path integration of a quadratic action with a generalized memory

Using the promeasure technique, we give an alternative evaluation of a path integral corresponding to a quadratic action with a generalized memory.

Expression Profiling of Nucleotide Metabolism-Related Genes in Human Breast Cancer Cells After Treatment with 5-Fluorouracil

5-Fluorouracil (5-FU) is one of the most widely used drugs for treatment of cancers, including breast cancer that exhibits its anticancer activity by inhibiting DNA synthesis and also incorporated into DNA and RNA. The objective of this investigation was to find out the total nucleotide metabolism genes regulated by 5-FU in breast cancer cell line. The breast cancer cell line MCF-7 was treated with the drug 5-FU. To analyze the expression of genes, we have conducted the experiment using 1.7k and 19k human microarray slide and confirmed the expression of genes by semiquantitative reverse transcription-polymerase chain reaction. The expression of 44 genes involved in the nucleotide metabolism pathway was quantified. Of these 44 genes analyzed, transcription of 6 genes were upregulated and 9 genes were downregulated. Earlier studies revealed that the transcription of genes for key enzymes like thymidylate synthase, thymidinekinase, and dihydropyrimidine dehydrogenase are regulated by 5-FU. This study identified some novel genes like thioredoxin reductase, ectonucleotide triphosphate dephosphorylase, and CTP synthase are regulated by 5-FU. The data also reveal large-scale perturbation in transcription of genes not involved directly in the known mechanism of action of 5-FU.

Topochemical photodimerization of 7-acetoxycoumarin: the acetoxy group as a steering agent

Among the various substituted coumarins investigated only 7-acetoxycoumarin is observed to photodimerize topochemically in the crystalline state and this observation may be of importance in the context of "crystal engineering".

Comment on “path integration of a quadratic action with a generalized memory

Using the promeasure technique, we give an alternative evaluation of a path integral corresponding to a quadratic action with a generalized memory.

Linalyl Acetate Is Metabolized by Pseudomonas incognita with the Acetoxy Group Intact

Metabolism of linalyl acetate by Pseudomonas incognita isolated by enrichment culture on the acyclic monoterpene alcohol linalool was studied. Biodegradation of linalyl acetate by this strain resulted in the formation of linalool, linalool- 8-carboxylic acid, oleuropeic acid, and A5-4-acetoxy-4-methyl hexenoic acid. Cells adapted to linalyl acetate metabolized linalyl acetate-8-aldehyde to linalool- 8-carboxylic acid, linalyl acetate-8-carboxylic acid, A5-4-acetoxy-4-methyl hexenoic acid, and geraniol-8-carboxylic acid. Resting cell suspensions previously grown with linalyl acetate oxidized linalyl acetate-8-aldehyde to linalyl acetate-8- carboxylic acid, A5-4-acetoxy-4-methyl hexenoic acid, and pyruvic acid. The crude cell-free extract (10,000 g of supernatant), obtained from the sonicate of linalyl acetate-grown cells, was shown to contain enzyme systems responsible for the formation of linalyl acetate-8-carboxylic acid and linalool-8-carboxylic acid from linalyl acetate. The same supernatant contained NAD-linked alcohol and aldehyde dehydrogenases involved in the formation of linalyl acetate-8-aldehyde and linalyl acetate-8-carboxylic acid, respectively. On the basis of various metabolites isolated from the culture medium, resting cell experiments, growth and manometric studies carried out with the isolated metabolites as well as related synthetic analogs, and the preliminary enzymatic studies performed with the cellfree extract, a probable pathway for the microbial degradation of linalyl acetate with the acetoxy group intact is suggested.