Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread Indo-Pacific three-spot damselfish, Dascyllus trimaculatus, and closely related D. auripinnis

A set of 13 simple sequence repeat markers was developed from D. trimaculatus genomic DNA, tested for D. auripinnis and characterized using 40 individuals per species. All the loci were polymorphic with a number of alleles ranging from three to 30. Observed heterozygosities varied from 0.23 to 0.89 for D. trimaculatus and from 0.11 to 0.85 for D. auripinnis. Early results show that these will be powerful markers for the study of ecological and evolutionary mechanism in this coral reef fish species complex.     

Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos

Polycomb group (PcG) and trithorax group (trxG) proteins are conserved chromatin factors that regulate key developmental genes throughout development. In Drosophila, PcG and trxG factors bind to regulatory DNA elements called PcG and trxG response elements (PREs and TREs). Several DNA binding proteins have been suggested to recruit PcG proteins to PREs, but the DNA sequences necessary and sufficient to define PREs are largely unknown. Here, we used chromatin immunoprecipitation (ChIP) on chip assays to map the chromosomal distribution of Drosophila PcG proteins, the N- and C-terminal fragments of the Trithorax (TRX) protein and four candidate DNA-binding factors for PcG recruitment. In addition, we mapped histone modifications associated with PcG-dependent silencing and TRX-mediated activation. PcG proteins colocalize in large regions that may be defined as polycomb domains and colocalize with recruiters to form several hundreds of putative PREs. Strikingly, the majority of PcG recruiter binding sites are associated with H3K4me3 and not with PcG binding, suggesting that recruiter proteins have a dual function in activation as well as silencing. One major discriminant between activation and silencing is the strong binding of Pleiohomeotic (PHO) to silenced regions, whereas its homolog Pleiohomeotic-like (PHOL) binds preferentially to active promoters. In addition, the C-terminal fragment of TRX (TRX-C) showed high affinity to PcG binding sites, whereas the N-terminal fragment (TRX-N) bound mainly to active promoter regions trimethylated on H3K4. Our results indicate that DNA binding proteins serve as platforms to assist PcG and trxG binding. Furthermore, several DNA sequence features discriminate between PcG- and TRX-N–bound regions, indicating that underlying DNA sequence contains critical information to drive PREs and TREs towards silencing or activation.     

Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci

We carried out genome-wide association (GWA) studies in inbred mouse strains characterized for their lung tumor susceptibility phenotypes (spontaneous or urethane-induced) with panels of 12,959 (13K) or 138,793 (140K) single-nucleotide polymorphisms (SNPs). Above the statistical thresholds, we detected only SNP rs3681853 on Chromosome 5, two SNPs in the pulmonary adenoma susceptibility 1 (Pas1) locus, and SNP rs4174648 on Chromosome 16 for spontaneous tumor incidence, urethane-induced tumor incidence, and urethane-induced tumor multiplicity, respectively, with the 13K SNP panel, but only the Pas1 locus with the 140K SNP panel. Haplotype analysis carried out in the latter panel detected four additional loci. Loci reported in previous GWA studies failed to replicate. Genome-wide genetic linkage analysis in urethane-treated (BALB/c×C3H/He)F2, (BALB/c×SWR/J)F2, and (A/J×C3H/He)F2 mice showed that Pas1, but none of the other loci detected previously or herein by GWA, had a significant effect. The Lasc1 gene, identified by GWA as a functional element (Nat. Genet., 38:888–95, 2006), showed no genetic effects in the two independent intercross mouse populations containing both alleles, nor was it expressed in mouse normal lung or lung tumors. Our results indicate that GWA studies in mouse inbred strains can suffer a high rate of false-positive results and that such an approach should be used in conjunction with classical linkage mapping in genetic crosses.     

Identification of an achiral analogue of J-113397 as potent nociceptin/orphanin FQ receptor antagonist

To date, J-113397 represents the most potent and selective non peptide NOP receptor antagonist widely used in pharmacological studies. However, the synthesis, purification, and enantiomer separation of this molecule, which contains two chiral centers, is rather difficult and low-yielding. Here, we synthesized and tested a series of simplified J-113397 analogues to investigate the importance of the stereochemistry and the influence of the substituents at position 3 of the piperidine nucleus and on the nitrogen atom of the benzimidazolidinone nucleus. The compound coded as Trap-101, an achiral analogue of J-113397, combines a pharmacological profile similar to that of the parent compound with a practical, high-yielding preparation.     

Oxidative Stress in Normal‐Weight Obese Syndrome

The normal‐weight obese (NWO) syndrome was identified in women whose body weight (BW) and BMI are normal but whose fat mass (FM) is >30%. In these subjects, an early inflammatory status has been demonstrated. The aim was to verify whether oxidative stress occurs in NWO. Sixty age‐matched white Italian women were studied and subdivided as follows: 20 normal‐weight individuals (NW) (BMI <25 kg/m²; FM% <30%); 20 NWO (BMI <25 kg/m²; FM% >30%); 20 preobese‐obese (OB) (BMI >25 kg/m²; FM% >30%). Anthropometric, body composition (by dual‐energy X‐ray absorptiometry) variables, plasma levels of some cytokines, reduced glutathione (GSH), lipid hydroperoxide (LOOH), nitric oxide (NO) metabolites (NO₂^?/NO₃^?), antioxidant nonproteic capacity (ANPC) were measured and compared between groups. Glucose and lipid metabolism parameters were assessed. GSH and NO₂^?/NO₃^? levels resulted lower in OB and NWO compared to NW (P < 0.01). LOOH levels resulted higher in OB and NWO (P < 0.01). ANPC in NWO was lower than NW but higher with respect to OB (P < 0.01). Correlation analysis revealed strong associations between GSH levels and BW, BMI, FM% (R = ?0.45, at least P < 0.05); waist circumference (W) (R = ?0.33, P < 0.05); FFM% (R = 0.45, P < 0.01); IL‐1α, IL‐6, IL‐10, IL‐15 (R = ?0.39, ?0.33, ?0.36 ?0.34, respectively, P < 0.05); triglycerides (R = ?0.416, P < 0.05). LOOH levels were negatively related to FFM% (R = ?0.413, P < 0.05) and positively to FM%, IL‐15, TNF‐α, insulin, total cholesterol, low‐density lipoprotein cholesterol, and triglycerides (R = 0.408, R = 0.502, R = 0.341, R = 0.412, R = 0.4036, R = 0.405, R = 0.405, respectively, P < 0.05). The study clearly indicates that NWO, besides being in early inflammatory status, are contextually exposed to an oxidative stress related to metabolic abnormalities occurring in obesity.     

The Young,the Weak and the Sick: Evidence of Natural Selection by Predation

It is assumed that predators mainly prey on substandard individuals, but even though some studies partially support this idea, evidence with large sample sizes, exhaustive analysis of prey and robust analysis is lacking. We gathered data from a culling program of yellow-legged gulls killed by two methods: by the use of raptors or by shooting at random. We compared both data sets to assess whether birds of prey killed randomly or by relying on specific individual features of the prey. We carried out a meticulous post-mortem examination of individuals, and analysing multiple prey characteristics simultaneously we show that raptors did not hunt randomly, but rather preferentially predate on juveniles, sick gulls, and individuals with poor muscle condition. Strikingly, gulls with an unusually good muscle condition were also predated more than expected, supporting the mass-dependent predation risk theory. This article provides a reliable example of how natural selection may operate in the wild and proves that predators mainly prey on substandard individuals.     

Using coloured roots to study root interaction and competition in intercropped legumes and non-legumes

Aims Root interactions between neighbour plants represent a fundamental aspect of the competitive dynamics in pure stand and mixed cropping systems. The comprehension of such phenomena places big methodological challenges, and still needs clarification. The objectives of this work were (i) to test if a species with coloured roots can be used to examine the interaction in a legume-non-legume intercropping system; (ii) to verify the importance of initial root growth on the successive root development of mixture component plants; (iii) to test if the root interaction in the shallow layers has consequences for deep root growth and (iv) to compare the effect of intraspecific and interspecific competition on root development and biomass growth.Methods A detailed study on root growth and interaction was carried out using rhizotron tubes where two legume species were grown in pure stands or were intercropped with red beet, a variety of Beta vulgaris L. with clear red roots. Within the rhizotrons, the three species were grown either without competitors, with two plants of the same species to measure intraspecific competition or with one legume and one red beet plant to study interspecific competition. The use of mixtures where one component has clearly coloured roots, together with several scalar measurements of root depth and proliferation, allowed the measurement of the root system of each species when grown in the mixtures.Important findings The use of rhizotron tubes coupled with species with coloured roots represented a valuable method to study the belowground interaction in mixed cropping systems. The initial root growth was a very important feature for the subsequent dominance of a species and it was not related to seed dimension. Initial root growth was also important because the root interactions in the shallower soil layers were found to influence the root growth in deeper soil. The root system of the red beet showed much faster and deeper growth than that of the legumes, and made red beet the dominant component in the mixtures while the legume root system was confined to the shallower soil layer. Intraspecific competition was well tolerated by the legumes, but it was limiting for the highly competitive red beet. The outcome of root interaction between neighbour plants was confirmed to be species-specific as it changed according to the intensity of the competitive effect/response of each species of the mixture: both legumes were slightly affected by the intraspecific and highly affected by interspecific competition while red beet was more affected by intraspecific competition but strongly dominant when intercropped with legumes.