Evidence on the chromosomal location of centromeric DNA in Plasmodium falciparum from etoposide-mediated topoisomerase-II cleavage

Centromeres are the chromosomal loci that facilitate segregation, and, in most eukaryotes, they encompass extensive regions of genomic DNA. Topoisomerase-II has been identified as a crucial regulator of segregation in a wide range of organisms and exhibits premitotic accumulation at centromeres. Consistent with this property, treatment of cells with the topoisomerase-II inhibitor etoposide promotes chromosomal cleavage at sites within centromeric DNA. In the case of the human malaria parasite Plasmodium falciparum, despite a completed genome sequence, there are no experimental data on the nature of centromeres. To address this issue, we have used etoposide-mediated topoisomerase-II cleavage as a biochemical marker to map centromeric DNA on all 14 parasite chromosomes. We find that topoisomerase-II activity is concentrated at single chromosomal loci and that cleavage sites extend over approximately 10 kb. A shared feature of these topoisomerase-II cleavage sites is the presence of an extremely AT-rich ( approximately 97%) domain with a strictly defined size limit of 2.3-2.5 kb. Repetitive arrays identified within the domains do not display interchromosomal conservation in terms of length, copy number, or sequence. These unusual properties suggest that P. falciparum chromosomes contain a class of "regional" centromere distinct from those described in other eukaryotes, including the human host.

The suppression of galactose metabolism in Trypanosoma cruzi epimastigotes causes changes in cell surface molecular architecture and cell morphology

The cell surface of the epimastigote form of Trypanosoma cruzi is covered by glycoconjugates rich in galactose. The parasite cannot take up galactose through its hexose transporter, suggesting that the epimerisation of UDP-glucose to UDP-galactose may be the parasite's only route to this sugar. The T. cruzi UDP-glucose 4'-epimerase is encoded by the TcGALE gene. We were unable to make a CL-Brener strain T. cruzi epimastigote TcGALE-/- null mutant, suggesting that the gene is essential. Two TcGALE+/- single-allele knockout clones displayed aberrant morphology and haploid deficiency with respect to galactose metabolism. The morphological phenotypes included shortened flagella, increased incidence of spheromastigotes, agglutination and a novel walnut-like appearance. The reduced supply of UDP-galactose was manifest in the two clones as a six- or nine-fold reduction in the expression of galactopyranose-containing cell surface mucins and negligible or two-fold reduction in the expression of galactofuranose-containing glycoinositolphospholipids. The major loss of mucins as opposed to glycoinositolphospholipids may indicate that the latter are more important for basic parasite survival in culture. The apparent haploid deficiency suggests that epimerase levels are close to limiting, at least in the epimastigote form, and might be exploited as a potential drug target.

Immobilized alpha-melanocyte stimulating hormone 10-13 (GKPV) inhibits tumor necrosis factor-alpha stimulated NF-kappaB activity

alpha-MSH is an anti-inflammatory peptide which signals by binding to the melanocortin-1 receptor (MC1R) and elevating cyclic AMP in several different cells and tissues. The carboxyl terminal peptides of alpha-MSH (KPV/GKPV) are the smallest minimal sequences that prevent inflammation, but it is not known if they operate via MC1R or cyclic AMP. The aim of this study was to examine the intracellular signaling potential of the GKPV peptide sequence when immobilized to polystyrene beads via a polyethylene glycol moiety. Beads containing an immobilized GKPV peptide were investigated for their ability to inhibit proinflammatory tumor necrosis factor-alpha (TNF-alpha) stimulated activation of NF-kappaB in HBL cells stably transfected with an NF-kappaB-luciferase reporter construct. Peptide functionalized beads were compared with the ability of soluble peptide alone (alpha-MSH or GKPV) or non-functionalized beads to inhibit TNF-alpha stimulated activation of NF-kappaB. GKPV peptide functionalized beads significantly inhibited NF-kappaB-luciferase activity in comparison to beads containing no peptide moiety in one of two growths conditions investigated. Soluble alpha-MSH and GKPV peptides were also confirmed to inhibit NF-kappaB-luciferase. The present study suggests that the carboxyl terminal MSH peptide acts via a cell receptor-based mechanism and furthermore may support the potential use of such immobilized ligands for anti-inflammatory therapeutic use.

Functional characterisation of the iron superoxide dismutase gene repertoire in Trypanosoma brucei

Superoxide dismutases (SOD) are a family of antioxidant enzymes that function by removing superoxide anions from the cellular environment. Here, we show that the African trypanosome, Trypanosoma brucei, expresses four SOD isoforms, three of which we have validated biochemically as iron dependent, a feature normally associated with prokaryotic SODs. Localisation studies reveal that two of the enzymes are found predominantly in a parasite-specific organelle, the glycosome (TbSODB1 and TbSODB2), while the other two are targeted to the mitochondrion (TbSODA and TbSODC). Functional analysis of the SOD repertoire in bloodstream form parasites was performed using an inducible RNA interference (RNAi) approach. Down-regulation of the glycosomal SOD transcripts corresponded with a significant reduction in the corresponding proteins and a dramatic level of cell death within the population. The importance of one of the mitochondrial enzymes (TbSODA) only became apparent when parasites were exposed to the superoxide-generating agent paraquat following induction of RNAi. These experiments therefore identify essential components of the superoxide metabolising arm of the T. brucei oxidative defence system and validate these enzymes as parasite-specific targets for drug design.

Vitamin C biosynthesis in trypanosomes: a role for the glycosome

The capacity to synthesize vitamin C (ascorbate) is widespread in eukaryotes but is absent from humans. The last step in the biosynthetic pathway involves the conversion of an aldonolactone substrate to ascorbate, a reaction catalyzed by members of an FAD-dependent family of oxidoreductases. Here we demonstrate that both the African trypanosome, Trypanosoma brucei, and the American trypanosome, Trypanosoma cruzi, have the capacity to synthesize vitamin C and show that this reaction occurs in a unique single-membrane organelle, the glycosome. The corresponding T. brucei flavoprotein (TbALO) obeys Michaelis-Menten kinetics and can utilize both L-galactono-gamma-lactone and D-arabinono-gamma-lactone as substrate, properties characteristic of plant and fungal enzymes. We could detect no activity toward the mammalian enzyme substrate L-gulono-gamma-lactone. TbALO null mutants (bloodstream form) were found to display a transient growth defect, a trait that was enhanced when they were cultured in medium in which the essential serum component had been pretreated with ascorbate oxidase to deplete vitamin C. It is implicit, therefore, that bloodstream-form trypanosomes also possess a capacity for ascorbate transport.

Monitoring the effect of ultrafast deactivation of the electronic excited states of DNA bases and polynucleotides following 267 nm laser excitation using picosecond time-resolved infrared spectroscopy

In this paper we demonstrate the use of picosecond time-resolved infrared spectroscopy (ps-TRIR) to monitor the early structural dynamics of DNA bases and polydeoxynucleotides following UV excitation in solution.

Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional "strand-switch" domain as a major feature

Trypanosomatids are an ancient family that diverged from the main eukaryotic lineage early in evolution, which display several unique features of gene organization and expression. Although genome sequencing is now complete, the nature of centromeres in these and other parasitic protozoa has not been resolved. Here, we report the functional mapping of a centromere in the American trypanosome, Trypanosoma cruzi, a parasite with an unusual mechanism of genetic exchange that involves the generation of aneuploidy by nuclear hybridization. Using a telomere-associated chromosome fragmentation approach, we show that the region required for the mitotic stability of chromosome 3 encompasses a transcriptional "strand-switch" domain constituted by a 16-kb GC-rich island. The domain contains several degenerate retrotransposon-like insertions, but atypically, lacks the arrays of satellite repeats normally associated with centromeric regions. This unusual type of organization may represent a paradigm for centromeres in T. cruzi and other primitive eukaryotes.

Reduction of dipyrido-[3,2-a:2′,3′-c]-phenazine (dppz) by photolysis in ethanol solution

Photolysis of dipyrido-[3,2-a:2',3'-c]-phenazine (dppz) (1) in ethanol solution leads to the formation of 9,14-dihydrodipyridophenazine (2), which has been characterised by detailed NMR analysis, UV/VIS absorption spectroscopy, and theoretical calculations which reveal that its red colour is due to a low-lying intramolecular charge transfer state.

Photophysical study of a family of [Ru(phen)2(Mendpq)]2+ complexes in different solvents and DNA: a specific water effect promoted by methyl substitution

The synthesis and spectroscopic characterisation of a family of ruthenium complexes [Ru(phen)(2)(Me(n)dpq)](2+)(n= 0, 1, 2) are reported and the photophysical effect of the progressive methyl substitution on the dpq ligand ascertained in a range of solvents and in the presence of DNA: [Ru(phen)(2)(dpq)](2+)(1), [Ru(phen)(2)(Medpq)](2+)(2) and [Ru(phen)(2)(Me(2)dpq)](2+)(3)(where dpq is dipyrido[3,2-f:2',3'-h]-quinoxaline; Medpq is 2-methyldipyrido[3,2-f:2',3'-h]-quinoxaline; Me(2)dpq is 2,3-dimethyldipyrido[3,2-f:2',3'-h]-quinoxaline and phen is 1,10-phenanthroline). The increase in electron density following substitution renders the quinoxaline nitrogen atoms more basic in the ground state to yield pK(a) values of -1.9, -2.3, and -2.7 for 3, 2, and 1, respectively. The methyl groups have a pronounced effect on the excited state photophysics of 1-3. In organic solvents, the non-radiative decay constant correlates well with the solvent polarity parameter pi*, with the effect being more pronounced with increasing methyl substitution. On the contrary, in aqueous solution there is a ca. four-fold decrease in the non-radiative decay constant upon methyl substitution. This "specific water effect" may be explained in terms of deactivation of the excited state by hydrogen bonding interactions between water and the quinoxaline nitrogen atoms, which is reduced on moving from 1 to 3. The excited state lifetimes and luminescence intensities for substantially increase when bound to DNA in aerated aqueous solutions, with a six-fold increase, compared to a more moderate three-fold increase for 2 and 3.

Synthesis of N3- and 2-NH2-substituted 6,7-diphenylpterins and their use as intermediates for the preparation of oligonucleotide conjugates designed to target photooxidative damage on single-stranded DNA representing the bcr-abl chimeric gene

Two 17-mer oligodeoxynucleotide-5'-linked-(6,7-diphenylpterin) conjugates, 2 and 3, were prepared as photosensitisers for targeting photooxidative damage to a 34-mer DNA oligodeoxynucleotide (ODN) fragment 1 representing the chimeric bcr-abl gene that is implicated in the pathogenesis of chronic myeloid leukaemia (CML). The base sequence in the 17-mer was 3'G G T A G T T A T T C C T T C T T5'. In the first of these ODN conjugates (2) the pterin was attached at its N3 atom, via a -(CH2)3OPO(OH)- linker, to the 5'-OH group of the ODN. Conjugate 2 was prepared from 2-amino-3-(3-hydroxypropyl)-6,7-diphenyl-4(3H)-pteridinone 10, using phosphoramidite methodology. Starting material 10 was prepared from 5-amino-7-methylthiofurazano[3,4-d]pyrimidine 4 via an unusual highly resonance stabilised cation 8, incorporating the rare 2H,6H-pyrimido[6,1-b][1,3]oxazine ring system. In the characterisation of 10 two pteridine phosphazenes, 15 and 29, were obtained, as well as new products containing two uncommon tricyclic ring systems, namely pyrimido[2,1-b]pteridine (20 and 24) and pyrimido[1,2-c]pteridine (27). In the second ODN conjugate the linker was -(CH2)5CONH(CH2)6OPO(OH)- and was attached to the 2-amino group of the pterin. In the preparation of 3, the N-hydroxysuccinimide ester 37 of 2-(5-carboxypentylamino)-6,7-diphenyl-4(3H)-pteridinone was condensed with the hexylamino-modified 17-mer. Excitation of 36 with near UV light in the presence of the single-stranded target 34-mer, 5'T G A C C A T C A A T A A G14 G A A G18 A A G21 C C C T T C A G C G G C C3' 1 caused oxidative damage at guanine bases, leading to alkali-labile sites which were monitored by polyacrylamide gel electrophoresis. Cleavage was observed at all guanine sites with a marked preference for cleavage at G14. In contrast, excitation of ODN-pteridine conjugate 2 in the presence of 1 caused oxidation of the latter predominantly at G18, with a smaller extent of cleavage at G15 and G14 (in the double-stranded portion) and G21. These results contrast with our previous observation of specific cleavage at G21 with ruthenium polypyridyl sensitisers, and suggest that a different mechanism, probably one involving Type 1 photochemical electron transfer, is operative. Much lower yields were found with the ODN-pteridine conjugate 3, perhaps as a consequence of the longer linker between the ODN and the pteridine in this case.

Microwave induced preparation of a-axis oriented double-ended needle-shaped ZnO microparticles

Microwave irradiation of solutions of Zn(NO3)2 and urea provides a straightforward route to a-axis oriented crystals of needle-like morphology.

Structure, function and evolution of microbial adenylyl and guanylyl cyclases

Cells respond to signals of both environmental and biological origin. Responses are often receptor mediated and result in the synthesis of so-called second messengers that then provide a link between extracellular signals and downstream events, including changes in gene expression. Cyclic nucleotides (cAMP and cGMP) are among the most widely studied of this class of molecule. Research on their function and mode of action has been a paradigm for signal transduction systems and has shaped our understanding of this important area of biology. Cyclic nucleotides have diverse regulatory roles in both unicellular and multicellular organisms, highlighting the utility and success of this system of molecular communication. This review will examine the structural diversity of microbial adenylyl and guanylyl cyclases, the enzymes that synthesize cAMP and cGMP respectively. We will address the relationship of structure to biological function and speculate on the complex origin of these crucial regulatory molecules. A review is timely because the explosion of data from the various genome projects is providing new and exciting insights into protein function and evolution.

The amino terminal domain of a novel WD repeat protein from Trypanosoma cruzi contains a non-canonical mitochondrial targeting signal

WD (tryptophan/aspartic acid) repeat proteins perform a wide variety of functions in eukaryotic cells. They are characterised by the presence of a number of conserved repeat motifs that contribute to the beta-propeller structures which are the common feature of this large group of proteins. We report here the properties of the first characterised member of this family in the American trypanosome, Trypanosoma cruzi (TcBPP1). In the CL Brener clone the protein is 482 amino acids long and is predicted to contain four WD repeat motifs, flanked by amino and carboxyl terminal extensions. TcBPP1 is a single copy gene present on a 1.0/1.6 Mb pair of homologous chromosomes in a locus that is syntenic with the corresponding regions of Trypanosoma brucei and Leishmania major chromosomes. Consistent with the proposed hybrid nature of the CL Brener clone, the proteins encoded by the two different alleles share only 97% identity at the amino acid level. To determine subcellular location, we examined transfected parasites for the distribution of green fluorescent protein (GFP) fused with different regions of TcBPP1. These studies demonstrated that a 115 amino acid peptide derived from the amino terminal domain of TcBPP1 is able to target GFP to the mitochondrion. Interestingly this region lacks a typical amino terminal presequence suggesting that mitochondrial import is mediated by an alternative targeting signal.

[Ru(TAP)2(dppz)]2+: a DNA intercalating complex, which luminesces strongly in water and undergoes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate

The lowest excited state of [Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine) 1 is strongly luminescent, even in water, and very oxidizing. Therefore it is able to oxidise not only guanosine-5'-monophosphate (GMP), as demonstrated by laser flash photolysis, but also guanine-containing polynucleotides such as calf thymus DNA and [poly(dG-dC)]2. The luminescence quenching was found to be faster in H2O than in D2O, as is the back reaction, indicating that both processes probably proceed by proton-coupled electron transfer. These properties, that are controlled by the triplet MLCT state in which the charge has been transferred from the Ru to a TAP ligand, contrast with those of the well known [Ru(phen)2(dppz)]2+ 2.

In Situ Dynamics of Phosphorus in the Rhizosphere Solution of Five Species

Root activity can modify the chemistry of the rhizosphere and alter phosphorus (P) availability and uptake. However, until recently, relatively little was known about the dynamics of soil solution P at the root surface because of our inability to measure in situ changes in solution P at the plant root. A mini-rhizotron experiment with corn (Zea mays L. cv. Stine 2250), soybean [Glycine max (L.) Merr. cv. Pioneer 3563), cottonwood (Populus deltoids L.), smooth brome (Bromus inermis Leyss.), and switchgrass (Panicum virgatum L.) was conducted to measure the spatial and temporal dynamics of P in the rhizosphere solution of a fine silty, P-rich calcareous soil (solid-phase total P concentration = 62 mg kg(-1), pH = 7.68) from western Iowa. Micro-suction cups were used to collect samples of soil solution from defined segments of the rhizosphere, and capillary electrophoresis (CE) was used to determine the P concentration of the soil solution. At the end of 10 d, a decreasing P concentration gradient in soil solution toward the root was observed in corn, cottonwood, and smooth brome. No clear rhizosphere effect was observed for soybean and switchgrass. Statistical analysis indicated significantly lower solution P concentrations in the rhizospheres of corn (p = 0.05), cottonwood (p = 0.01), and smooth brome (p = 0.01) compared with bulk soil solution. Results indicate that P depletion from rhizosphere soil solution depends on plant species. Under the conditions of this study, corn, cottonwood, and smooth brome were more effective in depleting solution P than soybean and switchgrass.

Enhanced third-order optical nonlinearity of silver nanoparticles with a tunable surface plasmon resonance

Poly(vinylalcohol) (PVA)-stabilized silver nanoparticles were prepared by a seeding method. Nanoparticles of varying morphology were obtained by controlled variation of the reaction conditions, and this method allowed the tailoring of the position of the surface plasmon resonance. The samples show two bands in the visible absorption spectrum: one in the 410-440-nm region and a second peak between 500 and 600 nm. This tunable surface plasmon resonance serves to increase the third-order optical nonlinearity (chi 3) of the nanoparticles (measured at 532 nm) by a factor of 16.

Magnetic nanoparticle assemblies on denatured DNA show unusual magnetic relaxivity and potential applications for MRI

Denatured (substantially single-stranded) herring sperm DNA acts as a template for the preparation of magnetic nanowires, forming stable aqueous suspensions, which exhibit unprecedentedly high relaxivity at low field, suggesting that the material may be a potentially useful reagent for MRI.