A model for pathogen population structure with cross-protection depending on the extent of overlap in antigenic variant repertoires

The persistence of discrete antigenic types among pathogens with multiple immunogenic loci can be explained by the action of immune-mediated competition. It has previously been shown that pathogen populations will self-organize into non-overlapping subsets of antigenic variants if cross-protection between pathogen types sharing any variants is high. Here, we examine the critical question of whether such strain structure will emerge if the degree of immune-mediated competition is dependent on the number of variants shared between pathogen types, rather than in an all-or-nothing manner. Our analysis uncovers a progression from no strain structure through to discrete stable strain structure through intermediate partially structured states. This suggests that the number of loci or epitope regions required to detect linkage disequilibrium (as a manifestation of stable discrete strain structure) in pathogen populations correlates inversely with the strength of immune selection.     

Mapping and tagging of seed coat colour and the identification of microsatellite markers for marker-assisted manipulation of the trait in Brassica juncea

Microsatellite marker technology in combination with three doubled haploid mapping populations of Brassica juncea were used to map and tag two independent loci controlling seed coat colour in B. juncea. One of the populations, derived from a cross between a brown-seeded Indian cultivar, Varuna, and a Canadian yellow-seeded line, Heera, segregated for two genes coding for seed coat colour; the other two populations segregated for one gene each. Microsatellite markers were obtained from related Brassica species. Three microsatellite markers (Ra2-A11, Na10-A08 and Ni4-F11) showing strong association with seed coat colour were identified through bulk segregant analysis. Subsequent mapping placed Ra2-A11 and Na10-A08 on linkage group (LG) 1 at an interval of 0.6 cM from each other and marker Ni4-F11 on LG 2 of the linkage map of B. juncea published previously (Pradhan et al., Theor Appl Genet 106:607–614, 2003). The two seed coat colour genes were placed with markers Ra2-A11 and Na10-A08 on LG 1 and Ni4-F11 on LG 2 based on marker genotyping data derived from the two mapping populations segregating for one gene each. One of the genes (BjSC1) co-segregated with marker Na10-A08 in LG 1 and the other gene (BjSC2) with Ni4-F11 in LG 2, without any recombination in the respective mapping populations of 130 and 103 segregating plants. The identified microsatellite markers were studied for their length polymorphism in a number of yellow-seeded eastern European and brown-seeded Indian germplasm of B. juncea and were found to be useful for the diversification of yellow seed coat colour from a variety of sources into Indian germplasm.     

A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function

A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era.     

Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion

Fibroblasts often constitute the majority of the stromal cells within a breast carcinoma, yet the functional contributions of these cells to tumorigenesis are poorly understood. Using a coimplantation tumor xenograft model, we demonstrate that carcinoma-associated fibroblasts (CAFs) extracted from human breast carcinomas promote the growth of admixed breast carcinoma cells significantly more than do normal mammary fibroblasts derived from the same patients. The CAFs, which exhibit the traits of myofibroblasts, play a central role in promoting the growth of tumor cells through their ability to secrete stromal cell-derived factor 1 (SDF-1); CAFs promote angiogenesis by recruiting endothelial progenitor cells (EPCs) into carcinomas, an effect mediated in part by SDF-1. CAF-secreted SDF-1 also stimulates tumor growth directly, acting through the cognate receptor, CXCR4, which is expressed by carcinoma cells. Our findings indicate that fibroblasts within invasive breast carcinomas contribute to tumor promotion in large part through the secretion of SDF-1.     

DNA-binding behavior of ruthenium(II) complexes containing both group 15 donors and 2,2':6',2''-terpyridine

Tetrafluoroborate salts of cationic ruthenium complexes [Ru(kappa(3)-tpy)(EPh(3))(2)Cl](+) (tpy=2,2':6',2'-terpyridine; E=P, 1 or As, 2) containing both the group 15 donor ligands and tpy and their representative substitution products are reported. Weak interaction {C-H...X (X=Cl, F and pi) and pi-pi interaction} studies revealed the presence of a double helical motif in complex 1, while the complex 2 assumes a single helical motif. Intercalative mode of interaction of the complexes 1 and 2 with calf thymus DNA (ctDNA) has been supported by absorption titration studies.     

Characterization of human immunodeficiency virus Gag-specific gamma interferon-expressing cells following protective mucosal immunization with alphavirus replicon particles

A safe, replication-defective viral vector that can induce mucosal and systemic immune responses and confer protection against many infectious pathogens, such as human immunodeficiency virus type 1 (HIV-1), may be an ideal vaccine platform. Accordingly, we have generated and tested alphavirus replicon particles encoding HIV-1 Gag from Sindbis virus (SIN-Gag) and Venezuelan equine encephalitis virus (VEE-Gag), as well as chimeras between the two (VEE/SIN-Gag). Following intramuscular (i.m.), intranasal (i.n.), or intravaginal (IVAG) immunization with VEE/SIN-Gag and an IVAG challenge with vaccinia virus encoding HIV Gag (VV-Gag), a larger number of Gag-specific CD8+ intracellular gamma interferon-expressing cells (iIFNEC) were detected in iliac lymph nodes (ILN), which drain the vaginal/uterine mucosa (VUM), than were observed after immunizations with SIN-Gag. Moreover, a single i.n. or IVAG immunization with VEE/SIN-Gag induced a larger number of cells expressing HIV Gag in ILN, and immunizations with VEE/SIN-Gag through any route induced better protective responses than immunizations with SIN-Gag. In VUM, a larger percentage of iIFNEC expressed alpha4beta7 or alpha(Ebeta)7 integrin than expressed CD62L integrin. However, in spleens (SP), a larger percentage of iIFNEC expressed alpha4beta7 or CD62L than expressed alpha(Ebeta)7. Moreover, a larger percentage of iIFNEC expressed the chemokine receptor CCR5 in VUM and ILN than in SP. These results demonstrate a better induction of cellular and protective responses following immunizations with VEE/SIN-Gag than that following immunizations with SIN-Gag and also indicate a differential expression of homing and chemokine receptors on iIFNEC in mucosal effector and inductive sites versus systemic lymphoid tissues.     

Municipal sludge leachate-induced genotoxicity in mice--a subacute study

Inappropriate disposal of municipal sludge (MS) results in the leaching of toxic metals and organic chemicals, which can contaminate the surface and ground water leading to the serious health hazards. In this study, the genotoxic potential of the leachate prepared from MS sample was examined in mouse bone marrow cells through chromosomal aberrations (CA), micronucleus test (MT) and comet assay. Analysis of metals and physicochemical parameters of the leachate was also carried out to correlate the genotoxic results. The dried sludge showed high concentrations of heavy metals, viz. Cr, Cu, Pb and Ni. However, in 10% leachate, concentrations of these metals were manifold lower than that of obtained in dried sludge. Male mice orally gavaged to leachates (0.1-0.4 ml/mouse/day) for 15 days revealed significant (P<0.01, P<0.001) inhibition of mitotic index (MI) and induction of chromatid/chromosome fragments and breaks in all the treatment groups. The effect was observed to be dose-dependent. Treatment of mice with leachates also induced significant (P<0.001) frequencies of micronucleated polychromatic erythrocytes (MNPCE). The results of comet assay revealed a statistically significant (P<0.05 and <0.01) DNA damage in bone marrow cells exposed to 0.2-0.4 ml/mouse/day. Findings of the present study indicate that the constant exposure of MS leachate can cause genotoxic effects in mammals and suggest risks in human population.     

Gene expression patterns of trembling aspen trees following long-term exposure to interacting elevated CO2 and tropospheric O3

Expression of 4600 poplar expressed sequence tags (ESTs) was studied over the 2001-2002 growing seasons using trees of the moderately ozone (O(3))-tolerant trembling aspen (Populus tremuloides) clone 216 exposed to elevated CO(2) and/or O(3) for their entire 5-yr life history. Based on replication of the experiment in years 2001 and 2002, 238 genes showed qualitatively similar expression in at least one treatment and were retained for analysis. Of these 238 genes, 185 were significantly regulated (1.5-fold) from one year to the other in at least one treatment studied. Less than 1% of the genes were regulated 2-fold or more. In the elevated CO(2) treatment, relatively small numbers of genes were up-regulated, whereas in the O(3) treatment, higher expression of many signaling and defense-related genes and lower expression of several photosynthesis and energy-related genes were observed. Senescence-associated genes (SAGs) and genes involved in the flavonoid pathway were also up-regulated under O(3), with or without CO(2) treatment. Interestingly, the combined treatment of CO(2) plus O(3) resulted in the differential expression of genes that were not up-regulated with individual gas treatments. This study represents the first investigation into gene expression following long-term exposure of trees to the interacting effects of elevated CO(2) and O(3) under field conditions. Patterns of gene-specific regulation described in this study correlated with previously published physiological responses of aspen clone 216.     

Arsenic accumulation of common plants from contaminated soils

A pot experiment was conducted to investigate the relationship between soluble concentrations of arsenic (As) in soil and its accumulation by maize (Zea mays), English ryegrass (Lolium perenne), rape (Brassica napus) and sunflower (Helianthus annuus) on two different soils: a calcareous Regosol (silty loam) and a non-calcareous Regosol (sandy loam). Arsenic (Na₂HAsO₄·7H₂O) was applied to obtain comparable soluble As concentrations in the two soils. In both soils, soluble As concentrations, extracted with 0.1 M NaNO₃, were found to correlate better with As concentrations in plants after 4 month of growth than total soil concentrations, extracted with 2 M HNO₃. With all four plant species, the relationship between the soluble As concentration in the soil and As that in the plants was non- linear, following Michaelis-Menten kinetics. Similar soluble As concentrations in the two soils did not result in a similar As concentration in the plants. Except for maize, arsenic transport from roots to shoots was significant, resulting in As concentrations in the leaves and grains above the Swiss tolerance limits for fodder and food crops (4 and 0.2 mg As kg^–1, respectively). Based on these results we suggest that beside As solubility, P availability and P demand, which are plant specific, have to be taken into account to predict the uptake of As by crop plants from As contaminated soils and to predict the risk of arsenic entering into the food chain.