Genetic structure of Pinus pinaster Ait. populations in Morocco revealed by nuclear microsatellites

Pinus pinaster is one of the most popular conifers used for reforestation in Morocco and represents an economically and ecologically important species for the region. In this study, nuclear microsatellites (ncSSRs) are used to compare genetic structure and diversity estimates of natural populations of Moroccan maritime pine. Samples were collected among 10 natural populations distributed in three biogeographically different regions, the Rif Mountain, the Middle and the High Atlas. Forty-five nuclear alleles at seven variable loci were found with a mean of 6.4 alleles per locus. A number of private alleles (17.1%) were shown in populations from Rif and Middle Atlas. Moreover, in Morocco, P. pinaster showed a lower genetic diversity than in other parts of its geographic range. Significant departures from Hardy–Weinberg equilibrium with excess homozygosity are observed indicating a high level of mating inside populations. Genetic diversity was structured with high variability among populations (Fst = 12%). Results show a correlation between genetic and geographic distances with an R-squared of 0.436. Two clusters were found using STRUCTURE, whereas three main clusters can be distinguished based on genetic distances of phylogenetic tree. Genetic relationships among maritime pine populations in Morocco appear to be related to historical, ecological as well as anthropogenic factors, suggesting the need for conservation strategies at the population level.     

Low-energy electron penetration range in liquid water

Monte Carlo simulations of electron tracks in liquid water are performed to calculate the energy dependence of the electron penetration range at initial electron energies between 0.2 eV and 150 keV, including the subexcitation electron region (<7.3 eV). Our calculated electron penetration distances are compared with available experimental data and earlier calculations as well as with the results of simulations using newly reported amorphous ice electron scattering cross sections in the range approximately 1-100 eV.     

Observation and measurement of internucleotide 2JNN coupling constants between 15N nuclei with widely separated chemical shifts

Scalar coupling correlations between hydrogen bonded 15N nuclei in non Watson–Crick base pairs is a critical step in the structure determination of unusual nucleic acids. For observing the 2JNN coupling constant between far upfield N2,N6 (amino) nitrogens and far downfield (N1,N3,N7) nitrogens (separated by 150–160 ppm), the HNN-COSY experiment (Dingley and Grzesiek, 1998) is rather insensitive, due to technical difficulties associated with simultaneous excitation of both extremes of the 15N spectrum. These nuclei may be correlated by treating them in a pseudo-heteronuclear manner, using 15N selective pulses. The wide chemical shift separation allows accurate measurement of the 2JNN coupling constant using spin-echo difference methods. Pulse sequences for observation and measurement of 2JNN coupling constants between amino and N7 nuclei are presented and demonstrated on an A-A mismatch segment of the uniformly (15N,13C) labelled DNA sample, d(GGAGGAT)2.     

Pulse sequences for detection of NH2···N hydrogen bonds in sheared G⋅A mismatches via remote, non-exchangeable protons

The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch.     

Organization of the chromosome region harboring a FLORICAULA/LEAFY gene in Liriodendron

FLORICAULA/LEAFY (FLO/LFY) plays an important role in the reproductive transition and controls flower spatial patterning by inducing the expression of the ABC floral organ identity genes. In this study, we sequenced two bacterial artificial chromosomes harboring a FLO/LFY and three other genes from yellow-poplar (Liriodendron tulipifera L.) and compared the gene order in this locus between several species. Besides the conserved terminal domains, key residues involved in interactions with DNA bases, backbone, and in dimerization were also conserved in the yellow-poplar FLO/LFY. Phylogenetic analysis of the FLO/LFY amino acid sequences placed yellow-poplar closer to eudicots than to monocotyledonous species. We found that gene content and order in this region of the yellow-poplar genome was more similar to corresponding regions in Vitis vinifera L., Carica papaya L., Populus trichocarpa Torr. & Gray, and Ricinus communis L., regardless of the evolutionary relationship. In addition, evidence for transposition, large insertions, and duplications were found, suggesting multiple and complex mechanisms of basal angiosperm genome evolution.     

Varied tolerance to NaCl salinity is related to biochemical changes in two contrasting lettuce genotypes

Salt stress perturbs a multitude of physiological processes such as photosynthesis and growth. To understand the biochemical changes associated with physiological and cellular adaptations to salinity, two lettuce varieties (Verte and Romaine) were grown in a hydroponics culture system supplemented with 0, 100 or 200 mM NaCl. Verte displayed better growth under 100 mM NaCl compared to Romaine, but both genotypes registered relatively similar reductions in growth under 200 mM NaCl treatment. Both varieties showed differences in net photosynthetic activity in the absence of salt and 8 days after salt treatment. These differences diminished subsequently under prolonged salt stress (14 days). Verte showed enhanced leaf proline and restricted total cations especially Na⁺, lesser malondialdehyde (MDA) formation and lignification in the roots under 100 mM NaCl salinity. Membrane damage estimated by electrolyte leakage increased with elevated salt concentrations in roots of both varieties, but Verte had significantly lower electrolyte leakage relative to Romaine under 100 mM NaCl. Moreover, Verte also accumulated greater levels of carotenoids under increasing NaCl concentrations compared to Romaine. Taken together, these findings suggest that the greater tolerance of Verte to 100 mM NaCl is related to the more restricted accumulation of total cations and toxic Na⁺ in the roots and enhanced levels of antioxidative metabolites in root and leaf tissue.     

Molecular evolutionary analyses of the Arabidopsis L7 ribosomal protein gene family

Cytoplasmic ribosomal protein (r-protein) genes in Arabidopsis thaliana are encoded by 80 multigene families that contain between two and seven members. Gene family members are typically similar at the protein sequence level, with the most divergent members of any gene family retaining 94% identity, on average. However, three Arabidopsis r-protein families - S15a, L7 and P2 - contain highly divergent family members. Here, we investigated the organization, structure, expression and molecular evolution of the L7 r-protein family. Phylogenetic analyses showed that L7 r-protein gene family members constitute two distinct phylogenetic groups. The first group including RPL7B, RPL7C and RPL7D has homologs in plants, animals and fungi. The second group represented by RPL7A is found in plants but has no orthologs from other fully-sequenced eukaryotic genomes. These two groups may have derived from a duplication event prior to the divergence of animals and plants. All four L7 r-protein genes are expressed and all exhibit a differential expression in inflorescence and flowers. RPL7A and RPL7B are less expressed than the other genes in all tissues analyzed. Molecular characterization of nucleic and protein sequences of L7 r-protein genes and analysis of their codon usage did not indicate any functional divergence. The probable evolution of an extra-ribosomal function of group 2 genes is discussed.