Recent advances in human quantitative-trait-locus mapping: comparison of methods for selected sibling pairs

During the past few years, there has been a great deal of new work on methods for mapping quantitative-trait loci by use of sibling pairs and sibships. There are several new methods based on linear regression, as well as several more that are based on score statistics. In theory, most of the new methods should be relatively robust to violations of distributional assumptions and to selected sampling, but, in practice, there has been little evaluation of how the methods perform on selected samples. We survey most of the new regression-based statistics and score statistics and propose a few minor variations on the score statistics. We use simulation to evaluate the type I error and the power of all of the statistics, considering (a) population samples of sibling pairs and (b) sibling pairs ascertained on the basis of at least one sibling with a trait value in the top 10% of the distribution. Most of the statistics have correct type I error for selected samples. The statistics proposed by Xu et al. and by Sham and Purcell are generally the most powerful, along with one of our score statistic variants. Even among the methods that are most powerful for "nice" data, some are more robust than others to non-Gaussian trait models and/or misspecified trait parameters.     

Pure partial trisomy 6p due to a familial insertion (16;6)(p12;p21.2p23)

There have only been eight patients with 6p pure trisomy involving different segments: four cases resulted from a translocation or insertion and four were due to an intrachromosomal duplication. We report here the first postnatally ascertained patient with a pure 6p partial trisomy due to an interchromosomal insertion (16;6)(p12;p21.2p23)mat. This rearrangement was confirmed by fluorescent in situ hybridization (FISH) with whole chromosome 6 and 16 painting probes. The clinical findings in the present patient were similar to those observed in previous cases, including craniofacial dysmorphism, minor anomalies, and lack of severe anatomical defects; yet, the unspecificity of many of these features prevented us from delineating the 6p pure trisomy syndrome.     

Parathyroid hormone regulation of type II sodium-phosphate cotransporters is dependent on an A kinase anchoring protein

Parathyroid hormone inhibits sodium-phosphate cotransport in proximal renal tubule cells through activation of several kinases. We tested the hypothesis that the activity of these kinases was coordinated by an A kinase anchoring protein (AKAP) by demonstrating that the type II sodium-phosphate cotransporter (NaPi-4) physically associated with an AKAP and that this association was necessary for regulation of phosphate transport by parathyroid hormone. Immunoprecipitation with anti-NaPi-4 antiserum and glutathione S-transferase pull-down with GST-NaPi-4 showed that NaPi-4 associated with AKAP79, protein kinase A catalytic and regulatory subunits, and the parathyroid hormone receptor in opossum kidney cells. When the regulatory subunit of protein kinase A was uncoupled from the AKAP by a competing peptide, parathyroid hormone lost the ability to inhibit phosphate transport. This result was confirmed by co-transfecting HEK293 cells with the sodium-phosphate cotransporter and wild type AKAP, a mutant AKAP79, or the empty vector. 8-Bromo-cAMP was able to inhibit phosphate transport in cells expressing the wild type AKAP79 but not empty vector or mutant AKAP79. We conclude that parathyroid hormone inhibits proximal renal tubule sodium-phosphate cotransport through a signaling complex dependent upon an AKAP.     

Effects of Inoculation with PGPR Bacillus and Pisolithus tinctorius on Pinus pinea L. Growth,Bacterial rhizosphere Colonization,and Mycorrhizal Infection

The effect of co-inoculation with Pisolithus tinctorius and a PGPR belonging to the genus Bacillus (Bacillus licheniformis CECT 5106 and Bacillus pumilus CECT 5105) in enhancing growth of Pinus pinea plants and the changes that occurred in rhizosphere microbial communities and the degree of mycorrhization were evaluated. Both bacterial strains of Bacillus promote the growth of Pinus pinea seedlings, but this biological effect does not imply a synergic effect with mycorrhizal infection. However, the positive response to mycorrhiza in a longer-term experiment it could be expected. The introduction of both inocula causes an lateration in the microbial rhizosphere composition, despite the low levels of inocula that were found at the end of the assay.     

Physiological characterization of Pseudomonas putida DOT-T1E tolerance to p-hydroxybenzoate

Pseudomonas putida DOT-T1E was isolated as a toluene-tolerant strain. We show that it is also able to grow on high concentrations (up to 17 g/liter [123 mM]) of p-hydroxybenzoate (4HBA). Tolerance to this aromatic carboxylic acid (up to 30 g/liter [217 mM]) is improved by preexposing the cells to low 4HBA concentrations; the adaptation process is caused by the substrate itself rather than by products resulting from its metabolism. The mechanisms of 4HBA tolerance seem to involve increased rigidity of the cell membrane as a result of a decrease in the cis/trans ratio of unsaturated fatty acids. In addition, energy-dependent efflux systems seem to operate in the exclusion of 4HBA from the cell membranes.     

Copper induction of lignin-modifying enzymes in the white-rot fungus Trametes trogii

Trametes trogii, a white rot basidiomycete involved in wood decay worldwide, produces several ligninolytic enzymes, laccase being the dominant one, with higher titers than those reported for most other white rot fungi studied up to date. The effect of copper on in vitro production of extracellular ligninolytic activities was studied. CuSO(4)·5H(2)O concentrations from 1.6 μM to 1.5 mM were tested in a synthetic medium with glucose 20 g/L and asparagine 3 g/L. The addition of copper (up to 1 mM) did not affect growth but strongly stimulated ligninolytic enzyme production; faster decolorization of the polymeric dye Poly R-478 was observed as well. Maximal production of manganese peroxidase, laccase, and glyoxal oxidase [1.28 U/mL, 93.8 U/mL (with a specific activity of 720 U/mg protein), and 0.46 U/mL respectively] was attained with 1 mM CuSO(4)·5H(2)O. However, higher copper concentrations inhibited growth and notably decreased manganese peroxidase production, although they did not affect laccase secretion. Laccase activity in the culture filtrate was maximal at 50 C and pH 3.4, and the enzyme was completely stable at pH 4.4 and above, and at 30 C for up to 5 d. Denaturing polyacrylamide gel electrophoresis of extracellular culture fluids showed two laccase activity bands (mol wt 38 and 60 kDa respectively). The pattern of isoenzyme production was not affected by medium composition but differed with culture age.     

Effects of water stress on antioxidant enzymes of leaves and nodules of transgenic alfalfa overexpressing superoxide dismutases

The antioxidant composition and relative water stress tolerance of nodulated alfalfa plants ( Medicago sativa L. ×  Sinorhizobium meliloti 102F78) of the elite genotype N4 and three derived transgenic lines have been studied in detail. These transgenic lines overproduced, respectively, Mn-containing superoxide dismutase (SOD) in the mitochondria of leaves and nodules, MnSOD in the chloroplasts, and FeSOD in the chloroplasts. In general for all lines, water stress caused moderate decreases in MnSOD and FeSOD activities in both leaves and nodules, but had distinct tissue-dependent effects on the activities of the peroxide-scavenging enzymes. During water stress, with a few exceptions, ascorbate peroxidase and catalase activities increased moderately in leaves but decreased in nodules. At mild water stress, transgenic lines showed, on average, 20% higher photosynthetic activity than the parental line, which suggests a superior tolerance of transgenic plants under these conditions. However, the untransformed and the transgenic plants performed similarly during moderate and severe water stress and recovery with respect to important markers of metabolic activity and of oxidative stress in leaves and nodules. We conclude that the base genotype used for transformation and the background SOD isozymic composition may have a profound effect on the relative tolerance of the transgenic lines to abiotic stress.