The apical caspase dronc governs programmed and unprogrammed cell death in Drosophila

Among the seven caspases encoded in the fly genome, only dronc contains a caspase recruitment domain. To assess the function of this gene in development, we produced a null mutation in dronc. Animals lacking zygotic dronc are defective for programmed cell death (PCD) and arrest as early pupae. These mutants present a range of defects, including extensive hyperplasia of hematopoietic tissues, supernumerary neuronal cells, and head involution failure. dronc genetically interacts with the Ced4/Apaf1 counterpart, Dark, and adult structures lacking dronc are disrupted for fine patterning. Furthermore, in diverse models of metabolic injury, dronc- cells are completely insensitive to induction of cell killing. These findings establish dronc as an essential regulator of cell number in development and illustrate broad requirements for this apical caspase in adaptive responses during stress-induced apoptosis.     

Optimization of genomic selection training populations with a genetic algorithm

In this article, we imagine a breeding scenario with a population of individuals that have been genotyped but not phenotyped. We derived a computationally efficient statistic that uses this genetic information to measure the reliability of genomic estimated breeding values (GEBV) for a given set of individuals (test set) based on a training set of individuals. We used this reliability measure with a genetic algorithm scheme to find an optimized training set from a larger set of candidate individuals. This subset was phenotyped to create the training set that was used in a genomic selection model to estimate GEBV in the test set. Our results show that, compared to a random sample of the same size, the use of a set of individuals selected by our method improved accuracies. We implemented the proposed training selection methodology on four sets of data on Arabidopsis, wheat, rice and maize. This dynamic model building process that takes genotypes of the individuals in the test sample into account while selecting the training individuals improves the performance of genomic selection models.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0116-6) contains supplementary material, which is available to authorized users.     

Genetic diversity of Vicia faba L. and Pisum sativum L. nodulating rhizobia in the central Black Sea region of Turkey

In this study, we obtained a total of 60 rhizobial isolates from root nodules of Vicia faba L. (n = 30) and Pisum sativum L. (n = 30) grown in the Central Black Sea region of Turkey. The 16S rDNA PCR-RFLP analysis with enzymes CfoI, HinfI, NdeII and MspI revealed a single pattern. Moreover, nucleotide sequence phylogenies based on both the 16S rDNA and recA suggested that these isolates belonged to Rhizobium leguminosarum. Phylogenetic analysis showed that some of our V. faba L.-originated isolates were closely related, indicating molecular evidence for the selection of some special R. leguminosarum bv. viciae isolates by V. faba L., as suggested in previous studies. Network analysis based on recA sequences revealed a common evolutionary history for Turkish, European, North and South American, and Jordanian R. leguminosarum bv. viciae isolates. We isolated four haplotypes using nodA and nifH nucleotide sequence data, i.e. four types of sym plasmids. Two of these types were common to rhizobial isolates from both V. faba L. and P. sativum L., indicating that nodulation factors may not be the mechanism for selection of the special R. leguminosarum bv. viciae populations by V. faba L.     

Taxonomic differentiation of Cupressus sempervirens and C. atlantica based on morphometric evidence

We investigated the interspecific morphological relationships of two related Mediterranean Cupressus taxa and the possible geographic differentiation of Eastern Mediterranean C. sempervirens using morphometric analysis. A total of 446 individuals, representing eight C. atlantica (Morocco) and 10 C. sempervirens (Greece, Turkey and Lebanon) populations were examined. The 17 morphological characters of cone, seed and shoot with leaves were measured and analysed statistically. Significant morphological differences between C. atlantica and C. sempervirens were detected for the majority of analysed characters. For C. sempervirens, significant differences were also detected and these were related to its three regions of origin, the Greek Islands, Taurus Mts and Lebanon Mts. Multivariate analyses did not indicate a clear geographic pattern of differentiation in C. sempervirens populations. A relatively low level of phenotypic differentiation was detected between populations originating from the Greek Islands and Taurus Mts. We also observed a moderate multivariate differentiation between the Lebanese and remaining C. sempervirens populations. Phenotypic differentiation detected in the Asian part of the C. sempervirens range reflects patterns of differentiation similar to those described for other taxa occurring in the Taurus and Lebanon Mts.     

Relationships among Cedrus libani, C. brevifolia and C. atlantica as revealed by the morphological and anatomical needle characters

The main aim of the present study was testing the value of the morphological and anatomical characteristics of the needles in distinguishing Cedrus atlantica, C. libani and C. brevifolia. Nine populations were sampled in their natural habit and 25 characters were used to describe the variation of the brachyblast needles and to analyze the differences between species. The results indicated that morphological and anatomical needle characters provide valuable tools in discrimination of the taxa. The scored differences were statistically significant, as revealed in the Tukey’s t test, discrimination analysis and hierarchical analysis of variation. The results support treating C. libani, C. atlantica and C. brevifolia as independent species.     

Pollen counts and their relationship to meteorological factors in Ankara,Turkey during 2005–2008

Pollen plays an important role in the development and exacerbation of allergic diseases. We aimed to investigate the days with highest counts of the most allergenic pollens and to identify the meteorological factors affecting pollen counts in the atmosphere of Ankara, Turkey. Airborne pollen measurements were carried out from 2005 to 2008 with a Burkard volumetric 7-day spore trap. Microscope counts were converted into atmospheric concentrations and expressed as pollen grains/m³. Meteorological parameters were obtained from the State Meteorological Service. All statistical analyses were done with pollen counts obtained from March to October for each year. The percentages of tree, grass and weed pollens were 72.1% (n = 24,923), 12.8% (n = 4,433) and 15.1% (n = 5,219), respectively. The Pinaceae family from tree taxa (39% to 57%) and the Chenopodiaceae/Amaranthaceae family from weed taxa, contributed the highest percentage of pollen (25% to 43%), while from the grass taxa, only the Poaceae family was detected from 2005 to 2008. Poaceae and Chenopodiaceae/Amaranthaceae families, which are the most allergenic pollens, were found in high numbers from May to August in Ankara. In multiple logistic regression analysis, wind speed (OR = 1.18, CI95% = 1.02–1.36, P = 0.023) for tree pollen, daily mean temperature (OR = 1.10, CI95% = 1.04–1.17, P = 0.001) and sunshine hours (OR = 1.15, CI95% = 1.01–1.30, P = 0.033) for grass pollen, and sunshine hours (OR = 3.79, CI95% = 1.03–13.92, P = 0.044) for weed pollen were found as significant risk factors for high pollen count. The pollen calendar and its association with meteorological factors depend mainly on daily temperature, sunshine hours and wind speed, which may help draw the attention of physicians and allergic patients to days with high pollen counts.     

IL-1α modulates neutrophil recruitment in chronic inflammation induced by hydrocarbon oil

Exposure to naturally occurring hydrocarbon oils is associated with the development of chronic inflammation and a wide spectrum of pathological findings in humans and animal models. The mechanism underlying the unremitting inflammatory response to hydrocarbons remains largely unclear. The medium-length alkane 2,6,10,14 tetramethylpentadecane (also known as pristane) is a hydrocarbon that potently elicits chronic peritonitis characterized by persistent infiltration of neutrophils and monocytes. In this study, we reveal the essential role of IL-1α in sustaining the chronic recruitment of neutrophils following 2,6,10,14 tetramethylpentadecane treatment. IL-1α and IL-1R signaling promote the migration of neutrophils to the peritoneal cavity in a CXCR2-dependent manner. This mechanism is at least partially dependent on the production of the neutrophil chemoattractant CXCL5. Moreover, although chronic infiltration of inflammatory monocytes is dependent on a different pathway requiring TLR-7, type I IFN receptor, and CCR2, the adaptor molecules MyD88, IL-1R-associated kinase (IRAK)-4, IRAK-1, and IRAK-2 are shared in regulating the recruitment of both monocytes and neutrophils. Taken together, our findings uncover an IL-1α-dependent mechanism of neutrophil recruitment in hydrocarbon-induced peritonitis and illustrate the interactions of innate immune pathways in chronic inflammation.