Fractioned DNA pooling: a new cost-effective strategy for fine mapping of quantitative trait loci

Selective DNA pooling (SDP) is a cost-effective means for an initial scan for linkage between marker and quantitative trait loci (QTL) in suitable populations. The method is based on scoring marker allele frequencies in DNA pools from the tails of the population trait distribution. Various analytical approaches have been proposed for QTL detection using data on multiple families with SDP analysis. This article presents a new experimental procedure, fractioned-pool design (FPD), aimed to increase the reliability of SDP mapping results, by "fractioning" the tails of the population distribution into independent subpools. FPD is a conceptual and structural modification of SDP that allows for the first time the use of permutation tests for QTL detection rather than relying on presumed asymptotic distributions of the test statistics. For situations of family and cross mapping design we propose a spectrum of new tools for QTL mapping in FPD that were previously possible only with individual genotyping. These include: joint analysis of multiple families and multiple markers across a chromosome, even when the marker loci are only partly shared among families; detection of families segregating (heterozygous) for the QTL; estimation of confidence intervals for the QTL position; and analysis of multiple-linked QTL. These new advantages are of special importance for pooling analysis with SNP chips. Combining SNP microarray analysis with DNA pooling can dramatically reduce the cost of screening large numbers of SNPs on large samples, making chip technology readily applicable for genomewide association mapping in humans and farm animals. This extension, however, will require additional, nontrivial, development of FPD analytical tools.     

Impact of Uncertainties in Exposure Assessment on Estimates of Thyroid Cancer Risk among Ukrainian Children and Adolescents Exposed from the Chernobyl Accident

The 1986 accident at the Chernobyl nuclear power plant remains the most serious nuclear accident in history, and excess thyroid cancers, particularly among those exposed to releases of iodine-131 remain the best-documented sequelae. Failure to take dose-measurement error into account can lead to bias in assessments of dose-response slope. Although risks in the Ukrainian-US thyroid screening study have been previously evaluated, errors in dose assessments have not been addressed hitherto. Dose-response patterns were examined in a thyroid screening prevalence cohort of 13,127 persons aged <18 at the time of the accident who were resident in the most radioactively contaminated regions of Ukraine. We extended earlier analyses in this cohort by adjusting for dose error in the recently developed TD-10 dosimetry. Three methods of statistical correction, via two types of regression calibration, and Monte Carlo maximum-likelihood, were applied to the doses that can be derived from the ratio of thyroid activity to thyroid mass. The two components that make up this ratio have different types of error, Berkson error for thyroid mass and classical error for thyroid activity. The first regression-calibration method yielded estimates of excess odds ratio of 5.78 Gy⁻¹ (95% CI 1.92, 27.04), about 7% higher than estimates unadjusted for dose error. The second regression-calibration method gave an excess odds ratio of 4.78 Gy⁻¹ (95% CI 1.64, 19.69), about 11% lower than unadjusted analysis. The Monte Carlo maximum-likelihood method produced an excess odds ratio of 4.93 Gy⁻¹ (95% CI 1.67, 19.90), about 8% lower than unadjusted analysis. There are borderline-significant (p = 0.101–0.112) indications of downward curvature in the dose response, allowing for which nearly doubled the low-dose linear coefficient. In conclusion, dose-error adjustment has comparatively modest effects on regression parameters, a consequence of the relatively small errors, of a mixture of Berkson and classical form, associated with thyroid dose assessment.     

The Dynamics of Naturally Acquired Immunity to Plasmodium falciparum Infection

Severe malaria occurs predominantly in young children and immunity to clinical disease is associated with cumulative exposure in holoendemic settings. The relative contribution of immunity against various stages of the parasite life cycle that results in controlling infection and limiting disease is not well understood. Here we analyse the dynamics of Plasmodium falciparum malaria infection after treatment in a cohort of 197 healthy study participants of different ages in order to model naturally acquired immunity. We find that both delayed time-to-infection and reductions in asymptomatic parasitaemias in older age groups can be explained by immunity that reduces the growth of blood stage as opposed to liver stage parasites. We found that this mechanism would require at least two components – a rapidly acting strain-specific component, as well as a slowly acquired cross-reactive or general immunity to all strains. Analysis and modelling of malaria infection dynamics and naturally acquired immunity with age provides important insights into what mechanisms of immune control may be harnessed by malaria vaccine strategists.     

Iodine-131 dose dependent gene expression in thyroid cancers and corresponding normal tissues following the chernobyl accident

The strong and consistent relationship between irradiation at a young age and subsequent thyroid cancer provides an excellent model for studying radiation carcinogenesis in humans. We thus evaluated differential gene expression in thyroid tissue in relation to iodine-131 (I-131) doses received from the Chernobyl accident. Sixty three of 104 papillary thyroid cancers diagnosed between 1998 and 2008 in the Ukrainian-American cohort with individual I-131 thyroid dose estimates had paired RNA specimens from fresh frozen tumor (T) and normal (N) tissue provided by the Chernobyl Tissue Bank and satisfied quality control criteria. We first hybridized 32 randomly allocated RNA specimen pairs (T/N) on 64 whole genome microarrays (Agilent, 4×44 K). Associations of differential gene expression (log(2)(T/N)) with dose were assessed using Kruskall-Wallis and trend tests in linear mixed regression models. While none of the genes withstood correction for the false discovery rate, we selected 75 genes with a priori evidence or P kruskall/P trend <0.0005 for validation by qRT-PCR on the remaining 31 RNA specimen pairs (T/N). The qRT-PCR data were analyzed using linear mixed regression models that included radiation dose as a categorical or ordinal variable. Eleven of 75 qRT-PCR assayed genes (ACVR2A, AJAP1, CA12, CDK12, FAM38A, GALNT7, LMO3, MTA1, SLC19A1, SLC43A3, ZNF493) were confirmed to have a statistically significant differential dose-expression relationship. Our study is among the first to provide direct human data on long term differential gene expression in relation to individual I-131 doses and to identify a set of genes potentially important in radiation carcinogenesis.     

A review of the spider genus Haplodrassus Chamberlin, 1922 in Crimea (Ukraine) and adjacent areas (Araneae, Gnaphosidae)

Eight species of Haplodrassus are recorded from Crimea: Haplodrassus bohemicus Miller & Buchar, 1977; Haplodrassus dalmatensis (L. Koch, 1866); Haplodrassus isaevi Ponomarev & Tsvetkov, 2006; Haplodrassus minor (O. P.-Cambridge, 1879); Haplodrassus kulczynskii Lohmander, 1942; Haplodrassus pseudosignifer Marusik, Hippa & Koponen, 1996; Haplodrassus signifer (C.L. Koch, 1839) and Haplodrassus umbratilis (L. Koch, 1866). The occurrence of Haplodrassus cognatus (Westring, 1861) in Crimea has not been confirmed. Haplodrassus bohemicus is a new species record for the Crimean fauna. Haplodrassus pseudosignifer is a new species record for Crimea and Ukraine as a whole, with Crimea as the westernmost point of its distribution range. Haplodrassus invalidus is recorded for the first time for the fauna of Azerbaijan, Caucasus and the former Soviet Union. Azerbaijan is the easternmost point of its known distribution range. All Crimean Haplodrassus species have only one peak of activity of adult specimens during the year. In Crimea we found syntopically two closely related species Haplodrassus dalmatensis and Haplodrassus isaevi in two localities (Sudak Distr., 10 km W Sudak, Mezhdurechie Vill., steppe; and Feodosiya Distr., Karadag Nature Reserve, steppes). These species differ in their phenology. The reproductive period of Haplodrassus dalmatensis isin May-July, and that of Haplodrassus isaevi occurs is in October-December. These phenological differences probably represent an additional mechanism of reproductive isolation between the two species. Diagnostic drawings are provided for all mentioned species as well as for Haplodrassus deserticola Schmidt & Krause, 1996 and Haplodrassus pugnans (Simon, 1880).     

Projection of the future EU forest CO2 sink as affected by recent bioenergy policies using two advanced forest management models

Forests of the European Union (EU) have been intensively managed for decades, and they have formed a significant sink for carbon dioxide (CO₂) from the atmosphere over the past 50 years. The reasons for this behavior are multiple, among them are: forest aging, area expansion, increasing plant productivity due to environmental changes of many kinds, and, most importantly, the growth rates of European forest having been higher than harvest rates. EU countries have agreed to reduce total emissions of GHG by 20% in 2020 compared to 1990, excluding the forest sink. A relevant question for climate policy is: how long will the current sink of EU forests be maintained in the near future? And could it be affected by other mitigation measures such as bioenergy? In this article we assess tradeoffs of bioenergy use and carbon sequestration at large scale and describe results of the comparison of two advanced forest management models that are used to project CO₂ emissions and removals from EU forests until 2030. EFISCEN, a detailed statistical matrix model and G4M, a geographically explicit economic forestry model, use scenarios of future harvest rates and forest growth information to estimate the future carbon balance of forest biomass. Two scenarios were assessed: the EU baseline scenario and the EU reference scenario (including additional bioenergy and climate policies). Our projections suggest a significant decline of the sink until 2030 in the baseline scenario of about 25–40% (or 65–125 Mt CO₂) compared to the models’ 2010 estimate. Including additional bioenergy targets of EU member states has an effect on the development of this sink, which is not accounted in the EU emission reduction target. A sensitivity analysis was performed on the role of future wood demand and proved the importance of this driver for the future sink development.     

Antagonistic Action of Lactobacilli and Bifidobacteria in Relation to Staphylococcus aureus and Their Influence on the Immune Response in Cases of Intravaginal Staphylococcosis in Mice

The antibacterial activity of Lactobacillus casei IMV B-7280, Lact. acidophilus IMV B-7279, Bifidobacterium longum VK1, and B. bifidum VK2 strains or their various compositions in relation to Staphylococcus aureus in vitro and on models of experimental intravaginal staphylococcosis of mice was determined. It was found that under the influence of these strains and their various compositions, the in vitro growth of Staph. aureus was inhibited, and the number of colonies of Staph. aureus plated from the vagina of infected mice was significantly reduced. The antibacterial activity of these strains separately and in compositions correlated with their ability to improve the performance of the immune response. These strains were the most effective in the following compositions: Lact. casei IMV B-7280-B. longum VK1-B. bifidum VK2. Strains of Lact. casei IMV B-7280, Lact. acidophilus IMV B-7279, B. bifidum VK2, and B. longum VK1 are prospective components of future probiotic drugs efficient in treating staphylococcosis and for immunity correction.     

Isolation of microsatellite and RAPD markers flanking the Yr15 gene of wheat using NILs and bulked segregant analysis.

Microsatellite and random amplified polymorphic DNA (RAPD) primers were used to identify molecular markers linked to the Yr15 gene which confer resistance to stripe rust (Puccina striiformis Westend) in wheat. By using near isogenic lines (NILs) for the Yr15 gene and a F2 mapping population derived from crosses of these lines and phenotyped for resistance, we identified one microsatellite marker (GWM33) and one RAPD marker (OPA19(800)) linked to Yr15. Then, bulked segregant analysis was used in addition to the NILs to identify RAPD markers linked to the target gene. Using this approach, two RAPD markers linked to Yr15 were identified, one in coupling (UBC199(700)) and one in repulsion phase (UBC212(1200)). After MAPMAKER linkage analysis on the F2 population, the two closest markers were shown to be linked to Yr15 within a distance of about 12 cM. The recombination rates were recalculated using the maximum likelihood technique to take into account putative escaped individuals from the stripe rust resistance test and obtain unbiased distance estimates. As a result of this study, the stripe rust resistance gene Yr15 is surrounded by two flanking PCR markers, UBC199(700) and GWM33, at about 5 cM from each side.     

The G protein-coupled receptor Gpr1 and the Galpha protein Gpa2 act through the cAMP-protein kinase A pathway to induce morphogenesis in Candida albicans

We investigated the role in cell morphogenesis and pathogenicity of the Candida albicans GPR1 gene, encoding the G protein-coupled receptor Gpr1. Deletion of C. albicans GPR1 has only minor effects in liquid hypha-inducing media but results in strong defects in the yeast-to-hypha transition on solid hypha-inducing media. Addition of cAMP, expression of a constitutively active allele of the Galpha protein Gpa2 or of the catalytic protein kinase A subunit TPK1 restores the wild-type phenotype of the CaGPR1-deleted strain. Overexpression of HST7, encoding a component of the mitogen-activated protein kinase pathway, does not suppress the defect in filamentation. These results indicate that CaGpr1 functions upstream in the cAMP-protein kinase A (PKA) pathway. We also show that, in the presence of glucose, CaGpr1 is important for amino acid-induced transition from yeast to hyphal cells. Finally, as opposed to previous reports, we show that CaGpa2 acts downstream of CaGpr1 as activator of the cAMP-PKA pathway but that deletion of neither CaGpr1 nor CaGpa2 affects glucose-induced cAMP signaling. In contrast, the latter is abolished in strains lacking CaCdc25 or CaRas1, suggesting that the CaCdc25-CaRas1 rather than the CaGpr1-CaGpa2 module mediates glucose-induced cAMP signaling in C. albicans.