Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass Sorghum bicolor

Patterns of linkage disequilibrium (LD) are of interest because they provide evidence of both equilibrium (e.g., mating system or long-term population structure) and nonequilibrium (e.g., demographic or selective) processes, as well as because of their importance in strategies for identifying the genetic basis of complex phenotypes. We report patterns of short and medium range (up to 100 kb) LD in six unlinked genomic regions in the partially selfing domesticated grass, Sorghum bicolor. The extent of allelic associations in S. bicolor, as assessed by pairwise measures of LD, is higher than in maize but lower than in Arabidopsis, in qualitative agreement with expectations based on mating system. Quantitative analyses of the population recombination parameter, rho, however, based on empirical estimates of rates of recombination, mutation, and self-pollination, show that LD is more extensive than expected under a neutral equilibrium model. The disparity between rho and the population mutation parameter, , is similar to that observed in other species whose population history appears to be complex. From a practical standpoint, these results suggest that S. bicolor is well suited for association studies using reasonable numbers of markers, since LD typically extends at least several kilobases but has largely decayed by 15 kb.     

What is needed for effective antitumor immunotherapy? Lessons learned using Listeria monocytogenes as a live vector for HPV-associated tumors

As a vaccine vector, Listeria monocytogenes targets the innate immune system, resulting in a cytokine response that enhances antigen-presenting cell function as well as inducing a Th1 profile. It also enhances cell-mediated immunity by targeting antigen delivery in antigen-presenting cells to both the MHC class I pathway of exogenous presentation that activates CD8 T cells and the MHC class II pathway that processes antigen endogenously and presents it to CD4 T cells. In this review, we describe the development of vaccine constructs that target the human papillomavirus 16 (HPV-16) E7 antigen, and we characterize their effects on tumor regression as well as various immune parameters both innate and adaptive. In particular, we describe the effect on tumor angiogenesis, induction of antitumor suppressor factors like CD4⁺CD25⁺ T cells and regulatory cytokines TGF- and IL-10, homing and infiltration of antigen-specific CD8⁺ T cells to the tumor, and also effects of the vaccines on antigen-presenting cells, especially focusing on dendritic cell maturation and ability to influence tumor regression. We believe that the identification of several immune parameters that correlate with antitumor efficacy, and of some that have a negative correlation, may have wider application for other cancer immunotherapeutic approaches.This article is a symposium paper from the second international conference Strategies for Immune Therapy, 29 February–3 March 2004, Würzburg, Germany; summarized by G. Pawelec and C. Gouttefangeas.     

Reduced atmospheric CO2 inhibits nitrogen mobilization in Festuca rubra

In defoliated grasses, where photosynthesis is reduced due to removal of leaf material, it is well established that remobilization of nitrogen occurs from both older remaining leaves and roots towards the younger growing leaves. In contrast, little is known about the movement of nitrogen within intact grass plants experiencing prolonged inhibition of photosynthesis. We tested the following hypotheses in Festuca rubra L. ssp. rubra cv. Boreal: that both reduction of the atmospheric CO2 concentration and defoliation (1) induce mobilization of nitrogen from roots and older leaves towards growing leaves and (2) elicit similar directional change in the abundance of proteins in roots and older leaves relevant to the process of nitrogen mobilization including, glutamine synthetase (GS), EC 6.3.1.2; papain, EC 3.4.22.2; chymopapain, EC 3.4.22.6; ribulose bisphosphate carboxylase/oxygenase (Rubisco), EC 4.1.1.39; and the light harvesting complex of photosystem II (LHCPII). After growth at ambient atmospheric CO2 concentration, plants of F. rubra were subject to atmospheres containing either ambient (350 micro l l-1) or deplete (< 20 micro l l-1) CO2. Concurrently, plants were either left intact or defoliated on one occasion. Steady state 15N labelling coupled with a series of destructive harvests over a 7-day period enabled changes in the nitrogen dynamics of the plants to be established. Proteins pertinent to the process of nitrogen mobilization were quantified by immunoblotting. Irrespective of defoliation, plants in ambient CO2 mobilized nitrogen from older to growing leaves. This mobilization was inhibited by deplete CO2. Greater concentration of Rubisco and reduced chymopapain abundance in older remaining leaves of intact plants, in deplete compared with ambient CO2, suggested the inhibition of mobilization was due to inhibition of protein degradation, rather than to the export of degradation products. Both deplete CO2 and defoliation induced nitrogen mobilization from roots to growing leaves. In plants at ambient CO2, defoliation did not affect nitrogen uptake or its allocation. Therefore in F. rubra nitrogen mobilization can occur independently of any downregulation of nitrogen uptake. This suggests either different signal compounds may act to downregulate uptake and upregulate mobilization, or if one particular signalling compound is used its concentration threshold differs for induction of mobilization and downregulation of uptake. The abundance of the cysteine proteases papain and chymopapain was low in roots suggesting that they were not involved in protein degradation in this tissue.     

Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes.

Quantitative trait loci (QTLs) affecting plant height and flowering were studied in the two Saccharum species from which modern sugarcane cultivars are derived. Two segregating populations derived from interspecific crosses between Saccharum officinarum and Saccharum spontaneum were genotyped with 735 DNA markers. Among the 65 significant associations found between these two traits and DNA markers, 35 of the loci were linked to sugarcane genetic maps and 30 were unlinked DNA markers. Twenty-one of the 35 mapped QTLs were clustered in eight genomic regions of six sugarcane homologous groups. Some of these could be divergent alleles at homologous loci, making the actual number of genes implicated in these traits much less than 35. Four QTL clusters controlling plant height in sugarcane corresponded closely to four of the six plant-height QTLs previously mapped in sorghum. One QTL controlling flowering in sugarcane corresponded to one of three flowering QTLs mapped in sorghum. The correspondence in locations of QTLs affecting plant height and flowering in sugarcane and sorghum reinforce the notion that the simple sorghum genome is a valuable "template" for molecular dissection of the much more complex sugarcane genome.     

Genetic characterization of heather (Calluna vulgaris (L.) hull) subject to different management regimes across great britain

Heather plants were collected from 34 populations in Great Britain, which differed according to their geographical location and associated management histories. Comparisons of differential grazing regimes were made across 10 sites in the first year of study, whereas the influence of differential burning regimes was considered at four sites during the second year. The extent of genetic variation, both within and between the selected heather populations, was examined using polymerase chain reaction (PCR)-based DNA fingerprinting methodologies. Initially, high genetic variation within populations obscured differences between populations. Heather stands that were geographically close proved to be genetically similar. Site latitude and longitude were strongly associated with genetic differences between heather populations; however, a range of grazing and burning management treatments had no consistent effect upon genetic diversity. The results represent the first national survey of genetic variation at the DNA level within UK populations of this important heathland species. They provided insights into the genetic structure of heather-dominated heathlands, revealing a lack of clonal dominance within populations, but rather a much more varied genetic makeup than might have been expected given the species' ability to propagate vegetatively. The processes that influence genetic diversity in heather populations are discussed, and the potential role of molecular techniques in heathland conservation is considered.     

No evidence for major histocompatibility complex-dependent mating patterns in a free-living ruminant population.

Conventionally, the extraordinary diversity of the vertebrate major histocompatibility complex (MHC is thought to have evolved in response to parasites and pathogens affecting fitness. More recently, reproductive mechanisms such as disassortative mating have been suggested as alternative mechanisms maintaining MHC diversity. A large unmanaged population of Soay sheep (Ovis aries L.) was used to investigate reproductive mechanisms in the maintenance of MHC diversity. Animals were sampled as new-born lambs and between 887 and 1209 individuals were typed at each of five microsatellite markers located either within or flanking the ovine MHC. All loci were in Hardy-Weinberg proportions. A novel likelihood-based approach was developed to analyse mating patterns using paternity data. No evidence for non-random mating with respect to MHC markers was found using this technique. We conclude that MHC diversity in the St Kildan Soay sheep population is unlikely to be maintained by mating preferences and that, in contrast with evidence from experimental mice populations, MHC variation plays no role in the mating structure of this population.     

Effect of 2-deoxy-D-glucose on mycotoxins from apples inoculated with Penicillium expansum

Patulin concentration was not significantly different in Bramley and Cox's apples inoculated with Penicillium expansum, and treated with the biocontrol enhancer 2-deoxy-D-glucose (DOG) when compared to no DOG treatment, despite average numerical increases. Some additional small HPLC peaks were detected from some extracts, one of which corresponded to citrinin. This revised version was published online in August 2006 with corrections to the Cover Date.