Persistence of sialodacryoadenitis virus in athymic rats

To determine whether SDAV infection persists in athymic rats, weanling athymic rats and euthymic rats were inoculated intranasally with 10(4) TCID50 of SDAV and examined periodically for up to 90 days. Viral antigen and lesions characteristic of acute SDAV infection, including rhinotracheitis, bronchitis and sialodacryoadenitis, were detected in both groups of rats during the first week. In euthymic rats, tissues were under repair and viral antigen was undetectable by day 17, and tissues were histologically normal by day 31 except for mild focal dacryoadenitis. In athymic rats, viral antigen and chronic active inflammation of respiratory tract, salivary and lacrimal glands persisted through day 90. Inflammation and viral antigen also were observed in the transitional epithelium of the renal pelvis and urinary bladder as late as day 90. Virus was isolated from nasopharynx, lung, salivary gland and Harderian gland of athymic rats through day 90. All euthymic rats seroconverted to SDAV by day 6, whereas all athymic rats remained seronegative through day 31, and two of six were seropositive by day 90. As judged by seroconversion of contact sentinels, six of six athymic rats shed virus through 6 weeks, and five of six through 10 weeks. These results indicate that SDAV persists in athymic rats, and that normal T cell function is required for host defenses against SDAV.     

Effect of gene conversion on variances of digenic identity measures

The variances and covariances of digenic descent measures are studied for a two-locus model incorporating mutation, gene conversion, recombination, drift, and finite sampling. Gene conversion can occur between allelic pairs of genes or between non-allelic pairs on the same or different gametes within individuals. Most interest therefore centers on pairs of genes, and five digenic identity measures are required. The behavior over time of these measures is studied, with an emphasis on the effects of gene conversion. Because of the stochastic nature of the forces of drift, recombination, mutation, and conversion, the actual identity status of gene pairs can vary from expectation among replicate populations. To study this variation we compute the expected variances and covariances of the measures, and show that this requires the introduction of trigenic and quadrigenic measures. Allowing for conversion between genes on different gametes requires a large number of these higher-order measures.     

Relationship between fertilization success and the number of milt donors in rainbow smelt Osmerus mordax (Mitchell): implications for population growth rates

A series of artificial fertilizations using rainbow smelt Osmerus mordax were conducted, each designed to assess the fertilization success of a female's eggs with milt from one to five males. Mean egg fertilization success increased and variance in fertilization success decreased when more males contributed to a constant volume of milt. This may indicate the presence of an Allee effect. The results suggest that potential changes in egg fertilization success due to a decrease in the number of males, in addition to changes in egg production due to a decrease in the number of females, can affect estimates of maximum sustainable harvest rates, and recovery of depleted populations.     

Winter commingling of populations of migratory species can cause breeding range underpopulation

We build a model with large-scale demographic consequences for migratory species. The model operates where four elements co-occur, and we rely on empirical research using migratory birds to demonstrate them. First, breeding ranges have internal structure flowing from natal philopatry. Second, fecundity varies geographically. Third, populations of different breeding provenances commingle during winter. And fourth, a population-limiting carrying capacity operates during winter. In the absence of breeding season population-limitation, only the breeding population with maximum fecundity persists. Consequently, some potential breeding areas that offer suitable and productive habitat are bereft of breeding birds because of the interplay between the geographical fecundity gradient and the shared winter quarters. Where breeding season population-limitation also plays a role for at least one population, one (or more) breeding population becomes permanently depressed, resulting in a density well below the carrying capacity of the productive breeding habitat that is occupied. In either case, not all populations fare equally well, despite net positive breeding season productivity. Changes in winter carrying capacity, for example habitat degradation in winter quarters, can lead to uneven effects on geographically defined breeding populations, even though there has been no change in the circumstances of the breeding range.     

Towards a reporter system to identify regulators of cross-talk between salicylate and jasmonate signaling pathways in Arabidopsis

The plant signaling hormones salicylic acid (SA) and jasmonic acid (JA) are regulators of inducible defenses that are activated upon pathogen or insect attack. Cross-talk between SA- and JA-dependent signaling pathways allows a plant to finely tune its response to the attacker encountered. In Arabidopsis, pharmacological experiments revealed that SA exerts a strong antagonistic effect on JA-responsive genes, such as PDF1.2, indicating that the SA pathway can be prioritized over the JA pathway. SA-mediated suppression of the JA-responsive PDF1.2 promoter was exploited for setting up a genetic screen aiming at the isolation of signal transduction mutants that are impaired in this cross-talk mechanism. The PDF1.2 promoter was fused to the herbicide resistance gene BAR to allow for life/death screening of a population of mutagenized transgenic plants. Non-mutant plants should survive herbicide treatment when methyl jasmonate (MeJA) is applied, but suppression of the JA response by SA should be lethal in combination with the herbicide. Conversely, crucial SA/JA cross-talk mutants should survive the combination treatment. SA effectively suppressed the expression of the PDF1.2::BAR transgene. However, suppression of the BAR gene did not result in suppression of herbicide resistance. Hence, a screening method based on quantitative differences in the expression of a reporter gene may be better suited to identify SA/JA cross-talk mutants. Here, we demonstrate that the PDF1.2::GUS reporter will be excellently suited in this respect.Key words: plant defense, salicylic acid, jasmonic acid, cross-talk, mutant screen, Arabidopsis     

GEIGER: investigating evolutionary radiations

SUMMARY: GEIGER is a new software package, written in the R language, to describe evolutionary radiations. GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Additionally, GEIGER's simulation algorithms can be used to analyze the statistical power of comparative approaches. AVAILABILITY: This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.     

Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study

Although prognostic gene expression signatures for survival in early-stage lung cancer have been proposed, for clinical application, it is critical to establish their performance across different subject populations and in different laboratories. Here we report a large, training-testing, multi-site, blinded validation study to characterize the performance of several prognostic models based on gene expression for 442 lung adenocarcinomas. The hypotheses proposed examined whether microarray measurements of gene expression either alone or combined with basic clinical covariates (stage, age, sex) could be used to predict overall survival in lung cancer subjects. Several models examined produced risk scores that substantially correlated with actual subject outcome. Most methods performed better with clinical data, supporting the combined use of clinical and molecular information when building prognostic models for early-stage lung cancer. This study also provides the largest available set of microarray data with extensive pathological and clinical annotation for lung adenocarcinomas.     

Unexpectedly Diverse Mesorhizobium Strains and Rhizobium leguminosarum Nodulate Native Legume Genera of New Zealand, while Introduced Legume Weeds Are Nodulated by Bradyrhizobium Species

The New Zealand native legume flora are represented by four genera, Sophora, Carmichaelia, Clianthus, and Montigena. The adventive flora of New Zealand contains several legume species introduced in the 19th century and now established as serious invasive weeds. Until now, nothing has been reported on the identification of the associated rhizobia of native or introduced legumes in New Zealand. The success of the introduced species may be due, at least in part, to the nature of their rhizobial symbioses. This study set out to address this issue by identifying rhizobial strains isolated from species of the four native legume genera and from the introduced weeds: Acacia spp. (wattles), Cytisus scoparius (broom), and Ulex europaeus (gorse). The identities of the isolates and their relationship to known rhizobia were established by comparative analysis of 16S ribosomal DNA, atpD, glnII, and recA gene sequences. Maximum-likelihood analysis of the resultant data partitioned the bacteria into three genera. Most isolates from native legumes aligned with the genus Mesorhizobium, either as members of named species or as putative novel species. The widespread distribution of strains from individual native legume genera across Mesorhizobium spp. contrasts with previous reports implying that bacterial species are specific to limited numbers of legume genera. In addition, four isolates were identified as Rhizobium leguminosarum. In contrast, all sequences from isolates from introduced weeds aligned with Bradyrhizobium species but formed clusters distinct from existing named species. These results show that native legume genera and these introduced legume genera do not have the same rhizobial populations.     

Carriage of Neisseria meningitidis and Neisseria lactamica among ethnic Greek school children from Russian immigrant families in Athens

During February and March 1995, a survey of meningococcal carriage in 625 school children was carried out in a suburb of Athens in which there was a large number of ethnic Greeks who had immigrated from Russia beginning in the early 1990s. The objectives of the study were: (1) to determine if factors associated with carriage of meningococci observed in a previous study of Greek school children were similar for the immigrant population; (2) to compare phenotypic characteristics of meningococci from the immigrant population with those isolated from children in Athens. Overall isolation rate for meningococci was 82/625 (13.1%), significantly higher than that found for school children in Athens (5.8%) during the winter of 1990 1991 (5.8%) (chi=25.98, P=0.0000003). By univariate analysis, carriage was not associated with sex, number of individuals per household, blood group, secretor status, socioeconomic level or maternal smoking; however, it was associated with fathers' smoking. The high proportion of men who smoked compared with the low proportion of women smokers might contribute to this finding. The main serogroup of meningococci isolated from this population was A (28%). While serogroup A appears to be more prevalent among Russian and Kurdish immigrants (14%) than among Greek school children or military recruits (4%), there has not been an increase in group A meningococcal disease in Greece. The isolation rate for N. lactamica was high 105/625 (17.3%). A few of these strains bound some of the monoclonal antibodies used for meningococcal serotyping and subtyping, and they are being examined in greater detail.     

Calibrating the avian molecular clock

Molecular clocks are widely used to date phylogenetic events, yet evidence supporting the rate constancy of molecular clocks through time and across taxonomic lineages is weak. Here, we present 90 candidate avian clock calibrations obtained from fossils and biogeographical events. Cross-validation techniques were used to identify and discard 16 inconsistent calibration points. Molecular evolution occurred in an approximately clock-like manner through time for the remaining 74 calibrations of the mitochondrial gene, cytochrome b . A molecular rate of approximately 2.1% (± 0.1%, 95% confidence interval) was maintained over a 12-million-year interval and across most of 12 taxonomic orders. Minor but significant variance in rates occurred across lineages but was not explained by differences in generation time, body size or latitudinal distribution as previously suggested.