New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.

Serum neutrophil gelatinase-associated lipocalin as a predictor of acute kidney injury in critically-ill neonates.

Early detection of evolving Acute Kidney Injury (AKI) in critically ill neonates can lead to better preventive and therapeutic interventions. Neutrophil Gelatinase-associated Lipocalin (NGAL) is a promising biomarker of AKI, which was also shown to increase in inflammation. The objective of this study was to assess the utility of serum NGAL (sNGAL) as an early marker of evolving AKI in critically-ill neonates with and without sepsis. sNGAL levels were estimated in 60 critically-ill neonates at the time of admission to Neonatal Intensive Care Unit (NICU), in comparison to 20 healthy matched control. Patients were categorized as sepsis (n = 35) and no-sepsis (n = 25) subgroups on basis of clinical and laboratory criteria. They were subsequently discriminated according to creatinine and urine output criteria of the Acute Kidney Injury Network (AKIN), into AKI (n = 34) and no-AKI (n = 26) subgroups, sNGAL levels were significantly higher in the patient group as compared to control (132.7 +/- 67.8 vs. 55 +/- 10.3 ng mL(-1), p = 0.0001). Elevated levels were comparable between sepsis and no-sepsis groups (130.1 +/- 69.4 vs. 136.5 +/- 66.6 ng mL(-1), p = 0.7) and they positively correlated with 48-hour post-admission serum creatinine (p = 0.0001). Patients of AKI group had significantly higher sNGAL than those of no-AKI group (176.2 +/- 55.9 vs. 75.9 +/- 28.3 ng mL(-1), p = 0.0001). A cut-off value for sNGAL of 117.5 ng mL(-1), was predictive of AKI with a sensitivity of 82% and a specificity of 88.5%. It could be speculated that measurement of serum NGAL can serve as a clinically useful marker for early prediction of evolving AKI in critically-ill neonates with and without sepsis.

Isolation and characterization of an endonuclease synthesized by barley (Hordeum vulgare L.) uninucleate microspores.

Few biochemical and molecular details are available on microspore growth and development. In this work, a nuclease was partially purified from diffusates of barley (Hordeum vulgare L.) microspores by using concanavalin-A as ligand. The chromatographic preparation contained a 34-kDa protein with nucleolytic activity; the enzyme (called BMN: barley microspore nuclease) was very stable at pH > 8.0 and temperatures below 50 degrees C. Activity was highest at pH 5.6 and increased almost exponentially with temperature until a breakpoint between activity and stability was reached at 70 degrees C. Although BMN was able to cleave RNA, the enzyme showed a remarkable preference for DNA, especially in the single-stranded form. The best homopolymeric substrates were poly(dA) and poly(A), whereas poly(dC), poly(G) and poly(I) were almost completely uncleaved. When incubated with intact nuclei, BMN caused a nucleosomal DNA ladder of approximately 200 bp. On the basis of DNA laddering, substrate specificity, Mg2+ -dependence and best performance at apoplastic pH, BMN can be referred to as a putative apoptotic nuclease involved in pollen development.