Mobility of short interspersed repeats within the chimpanzee lineage

The PV subfamily of Alu repeats in human DNA is largely composed of recently inserted members. Here we document additional members of the PV subfamily that are found in chimpanzee but not in the orthologous loci of human and gorilla, confirming the relatively recent and independent expansion of this Alu subfamily in the chimpanzee lineage. As further evidence for the youth of this Alu subfamily, one PV Alu repeat is specific to Pan troglodytes, whereas others are present in Pan paniscus as well. The A-rich tails of these Alu repeats have different lengths in Pan paniscus and Pan troglodytes. The dimorphisms caused by the presence and absence of PV Alu repeats and the length polymorphisms attributed to their A-rich tails should provide valuable genetic markers for molecular-based studies of chimpanzee relationships. The existence of lineage-specific Alu repeats is a major sequence difference between human and chimpanzee DNAs. Correspondence to: C.W. Schmid     

Phylogenetic isolation of a human alu flounder gene: Drift to new subfamily identity

A severe bottleneck in the size of the PV Alu subfamily in the common ancestor of human and gorilla has been used to isolate an Alu source gene. The human PV Alu subfamily consists of about one thousand members which are absent in gorilla and chimpanzee DNA. Exhaustive library screening shows that there are as few as two PV Alus in the gorilla genome. One is gorilla-specific, i.e., absent in the orthologous loci in both human and chimpanzee, suggesting the independent retrotranspositional activity of the PV subfamily in the gorilla lineage. The second of these two gorilla PV Alus is present in both human and chimpanzee DNAs and is the single PV Alu known to precede the radiation of these three species. The orthologous Alu in gibbon DNA resembles the next older Alu subfamily. Thus, this Alu locus is originally templated by a non-PV source gene and acquired characteristic PV sequence variants by mutational drift in situ, consequently becoming the first member and presumptive founder of this PV subfamily. Correspondence to: C.W. Schmid     

The impact of early adversity and education on genetic and brain morphological predictors of cognitive ability

Cognitive ability is a strong predictor of occupational achievement, quality of life and physical health. While variation in cognition is strongly heritable and has been robustly associated with early environment and brain morphology, little is known about how these factors combine and interact to explain this variation in cognition. To address this, we modelled the relationship between common genetic variation, grey matter volume, early life adversity and education and cognitive ability in a UK Biobank sample of N = 5237 individuals using structural equation modelling. We tested the hypotheses that total grey matter volume would mediate the association between genetic variation and cognitive ability, and that early life adversity and educational attainment would moderate this relationship. Common genetic variation, grey matter volume and early life adversity were each significant predictors in the model, explaining ~15% of variation in cognitive ability. Contrary to our hypothesis, grey matter volume did not mediate the relation between genetic variation and cognition performance. Neither did early life adversity or educational attainment moderate this relation, although educational attainment was observed to moderate the relationship between grey matter volume and cognitive performance. We interpret these findings in terms of the modest explanatory value of currently estimated polygenic scores accounting for variation in cognitive performance (~5%), making potential mediating and moderating variables difficult to confirm.     

Freeze-fracturing and surface labelling of embryonic neural retina cells

Freeze-fracturing of dissociated and aggregating neural retina cells from 7-day chick embryos revealed on the inner faces (PF) of the cell membrane numerous particles 6–20 nm in size. In contrast, the PF faces of blebs and some of the lobopodia that project from the cell surface were practically devoid of such particles. However, the elongated filopodia that abound on these cells showed numerous particles on their PF faces. These regional differences in the distribution of particles on PF faces of these cells are interpreted as reflecting membrane activity that leads to the formation of blebs and lobopodia. The frequent presence of “pits” at the basis of blebs and lobopodia is described. It is suggested that the “pits” are associated with the formation of these membrane projections; they may represent anchoring sites for microfilaments and for microtubules involved in the dynamic structure of the cell surface. ConA-binding sites on these cells were studied by scanning electron microscopy, using labeling with hemocyanin. The distribution of these sites on different regions of the cell surface coincided with the regional differences in the distribution of the inner membrane particles.     

Family studies of association between HLA and specific immune responses to highly purified pollen allergens

In 76 members of 13 large families, we investigated whether association exists between specific familialHLA haplotypes and immune responsiveness to four different highly purified pollen antigens (ragweed antigens E, Ra3, and Ra5 and rye grass Group I). Specific immune response was studied quantitatively by measurement of IgE-mediated skin sensitivity, serum IgG antibody, and antigen-induced lymphocyte proliferationin vitro. We found no evidence for association between specificHLA haplotype and specific response measured by any one or more of our indices of immune function. In several families we found evidence of specific response in one generation but not in another. We found a number of instances of individuals exhibiting lymphocyte responsiveness to an antigen, but no detectable specific IgE or IgG antibody. Surprisingly, we also found a few cases of individuals with marked IgE and/or IgG responses to a given antigen who showed no measurable lymphocyte responsiveness to that antigen, despite lymphocyte responsiveness to other nonimmunologically crossreacting antigens. In several cases, we also observed lymphocyte stimulation and serum IgG antibody, but no detectable IgE response. Our results conflict with previous investigators' reports of linkage betweenHLA haplotype and specific IgE-mediated skin sensitivity in families.HLA- linked immune response (Ir) loci may exist in humans, but genetic complexity and the limits of current technology preclude our ability to demonstrate their existence.     

Hippocampal 8-[3H]Hydroxy-2-(Di-n-Propylamino)Tetralin Binding Site Densities, Serotonin Receptor (5-HT1A) Messenger Ribonucleic Acid Abundance, and Serotonin Levels Parallel the Activity of the Hypothalamopituitary-Adrenal Axis in Rat

We have previously demonstrated that susceptibility of the Lewis rat to inflammatory disease, compared with the relatively resistant Fischer F344/N rat, is related to a hyporesponsive hypothalamopituitary-adrenal axis to inflammatory and other stress mediators. Because serotonin (5-HT) and the 5-HT1A receptor are important stimulators of this axis, we have investigated the levels of 8-[3H]-hydroxy-2,3-(di-n-propylamino)tetralin binding sites, 5-HT1A mRNA, 5-HT, and 5-hydroxyindoleacetic acid in various brain regions of Lewis, outbred Harlan Sprague Dawley, and Fischer F344/N rats. Lewis rats expressed significantly fewer hippocampal and frontal cortical 8-[3H]-hydroxy-2,3-(di-n-propylamino)tetralin binding sites and less 5-HT1A mRNA than Harlan Sprague Dawley and Fischer F344/N rats. Adrenalectomy increased the number of 8-[3H]hydroxy-2,3-(di-n-propylamino)tetralin binding sites and 5-HT1A mRNA expression in the hippocampus of all three strains. Levels of hippocampal 5-HT in Fischer F344/N rats were significantly greater than levels detected in the same regions from Lewis and Harlan Sprague Dawley rats. Hypothalamic 5-HT and 5-hydroxyindoleacetic acid levels in Harlan Sprague Dawley rats were higher than the same area from the other two strains. Adrenalectomy increased the levels of 5-hydroxyindoleacetic acid in the hypothalamus of all three strains. We conclude that hippocampal 5-HT1A receptor densities and 5-HT levels in the rat parallel the activity and responsiveness of the hypothalamopituitary-adrenal axis.     

Hemocyanin-derived phenoloxidase activity in the spiny lobster Panulirus argus (Latreille, 1804)

Hemocyanin and phenoloxidase belong to the type-3 copper protein family, sharing a similar active center whereas performing different roles. In this study, we demonstrated that purified hemocyanin (450 kDa) from the spiny lobster Panulirus argus shows phenoloxidase activity in vitro after treatment with trypsin, chymotrypsin and SDS (0.1% optimal concentration), but it is not activated by sodium perchlorate or isopropanol. The optimal pHs of the SDS-activated hemocyanin were 5.5 and 7.0. Hemocyanin from spiny lobster behaves as a catecholoxidase. Kinetic characterization using dopamine, L-DOPA and catechol shows that dopamine is the most specific substrate. Catechol and dopamine produced substrate inhibition above 16 and 2 mM respectively. Mechanism-based inhibition was also evidenced for the three substrates, being less significant for L-DOPA. SDS-activated phenoloxidase activity is produced by the hexameric hemocyanin. Zymographic analysis demonstrated that incubation of native hemocyanin with trypsin and chymotrypsin, produced bands of 170 and 190 kDa respectively, with intense phenoloxidase activity. Three polypeptide chains of 77, 80 and 89 kDa of hemocyanin monomers were identified by SDS-PAGE. Monomers did not show phenoloxidase activity induced by SDS or partial proteolysis.     

Above-ground biomass references for urban trees from terrestrial laser scanning data

Background and AimsWithin extending urban areas, trees serve a multitude of functions (e.g. carbon storage, suppression of air pollution, mitigation of the ‘heat island’ effect, oxygen, shade and recreation). Many of these services are positively correlated with tree size and structure. The quantification of above-ground biomass (AGB) is of especial importance to assess its carbon storage potential. However, quantification of AGB is difficult and the allometries applied are often based on forest trees, which are subject to very different growing conditions, competition and form. In this article we highlight the potential of terrestrial laser scanning (TLS) techniques to extract highly detailed information on urban tree structure and AGB.MethodsFifty-five urban trees distributed over seven cities in Switzerland were measured using TLS and traditional forest inventory techniques before they were felled and weighed. Tree structure, volume and AGB from the TLS point clouds were extracted using quantitative structure modelling. TLS-derived AGB estimates were compared with AGB estimates based on forest tree allometries dependent on diameter at breast height only. The correlations of various tree metrics as AGB predictors were assessed.Key ResultsEstimates of AGB derived by TLS showed good performance when compared with destructively harvested references, with an R² of 0.954 (RMSE = 556 kg) compared with 0.837 (RMSE = 1159 kg) for allometrically derived AGB estimates. A correlation analysis showed that different TLS-derived wood volume estimates as well as trunk diameters and tree crown metrics show high correlation in describing total wood AGB, outperforming tree height.ConclusionsWood volume estimates based on TLS show high potential to estimate tree AGB independent of tree species, size and form. This allows us to retrieve highly accurate non-destructive AGB estimates that could be used to establish new allometric equations without the need for extensive destructive harvesting.