Inferring relationships between pairs of individuals from locus heterozygosities

Background  

The traditional exact method for inferring relationships between individuals from genetic data is not easily applicable in all situations that may be encountered in several fields of applied genetics. This study describes an approach that gives affordable results and is easily applicable; it is based on the probabilities that two individuals share 0, 1 or both alleles at a locus identical by state.     

Erythropoietin-induced erythroid differentiation of K562 cells is accompanied by the nuclear translocation of phosphatidylinositol 3-kinase and intranuclear generation of phosphatidylinositol (3,4,5) trisphosphate.

D-3 phosphorylated inositides are a peculiar class of lipids, synthesized by phosphatidylinositol 3-kinase (PtdIns 3-K), which are also present in the nucleus. In order to clarify a possible role for nuclear D-3 phosphorylated inositides during human erythroid differentiation, we have examined the issue of whether or not, in K562 human erythroleukemia cells, erythropoietin (EPO) may generate nuclear translocation of an active PtdIns 3-K. Immunoprecipitation with an anti-p85 regulatory subunit of PtdIns 3-K, revealed that both the intranuclear amount and the activity of the kinase increased rapidly and transiently in response to EPO. Enzyme translocation was blocked by the specific PtdIns 3-K pharmacological inhibitor, LY294002, which also inhibited erythroid differentiation. In vivo, intranuclear synthesis of phosphatidylinositol (3,4,5) trisphosphate (PtdIns (3,4,5)P(3)) was stimulated by EPO. Almost all PtdIns 3-K that translocated to the nucleus was highly phosphorylated on tyrosine residues of the p85 regulatory subunit. These findings strongly suggest that an important step in the signaling pathways that mediate EPO-induced erythroid differentiation may be represented by the intranuclear translocation of an active PtdIns 3-K.     

Integrated analyses of litho- and biofacies in a Pliocene cyclothemic, alluvial to shallow marine succession (Tuscany, Italy)

Lithofacies analysis of the upper part of the Pliocene succession of the Valdelsa basin (central Italy) unravelled a number of depositional environments, ranging from alluvial plain to coastal, to marine. Strata are arranged in a hierarchy of elementary and composite unconformity-bounded units. A palaeoecological study of macro- (molluscs) and microfossils (pollen, dinocysts, foraminifera) allowed to finely reconstruct sub-environments within fine-grained terrestrial, coastal and marine deposits and thence to track the spatial and temporal change of physical conditions. The stacking pattern of sedimentary units highlights the lateral switching of onshore-offshore gradients and documents relative sea-level changes. These units are interpreted in a sequence stratigraphic framework. Elementary depositional sequences are arranged to form six composite depositional sequences, in turn encased within two major synthems. This hierarchy of unconformity-bounded sedimentary units suggests that sea-level variation has occurred at different time-frequencies. Glacio-eustasy and active tectonism are discussed as the main forcing factors regulating the different scales of sedimentary cyclicity.     

Morphological and phytochemical features of secretory structures in Hypericum richeri (Clusiaceae)

Structural and complementary chemical studies were carried out on Hypericum richeri , a lesser known species amongst those reported for folk medical use. We found only one type of secretory glands consisting of black dots which are present even in early emerging leaves. In the fully expanded leaves the nodular structure appears to be composed by a cluster of cells. These become unfunctional and disassembled towards the end of their development, and are used only as reservoirs of secretion products. HPTLC analyses showed that flower buds and flowers are the plant parts richest in active compounds. However, the spectrum of active compounds accumulated by H. richeri was both quantitatively and qualitatively similar to those reported for the pharmaceutically utilized, H. perforatum , and thus could potentially represent a possible alternative to this species.     

Quantifying the importance of geographic replication and representativeness when estimating demographic rates,using a coastal species as a case study

Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify how this lack of geographic representativeness can affect inferences about the global mean and variance of growth rates, which has implications for the robust design of a wide range of population studies. Using a coastal songbird, saltmarsh sparrow Ammodramus caudacutus, as a case study, we first estimated survival, fecundity, and population growth rates at 21 sites distributed across much of their breeding range. We then subsampled this large, representative dataset according to five sampling scenarios in order to simulate a variety of geographic biases in study design. We found spatial variation in demographic rates, but no large systematic patterns. Estimating the global mean and variance of growth rates using subsets of the data suggested that at least 10–15 sites were required for reasonably unbiased estimates, highlighting how relying on demographic data from just a few sites can lead to biased results when extrapolating across a species range. Sampling at the full 21 sites, however, offered diminishing returns, raising the possibility that for some species accepting some geographical bias in sampling can still allow for robust range‐wide inferences. The subsampling approach presented here, while conceptually simple, could be used with both new and existing data to encourage efficiency in the design of long‐term or large‐scale ecological studies.     

On the paleopathologic findings exhibited by the late Homo erectus of Ceprano, Italy

In March 1994, during excavation work for the construction of a motorway, a fragmented calvaria was discovered in the “Campo Grande” area near Ceprano, a town in southern Latium (Central Italy) about 55 miles from Rome. After reconstruction, the remain was recognized as belonging to aHomo erectus; it has been estimated that it goes back to the lowest middle Pleistocene. The calvaria exhibits two pathologic findings. The first is a congenital malformation of the sphenoidal sinus consisting in a deep, wide recess penetrating into the left greater wing as far as the sphenotemporal suture. The lesion was examined with the help of a cast whose features were compared with those described in some early and recent cases reported in the literature. The second finding is a healed, depressed fracture of the right brow ridge. The cause and mechanism of this lesion are discussed, and a mechanical approach has been used to provide information pertinent to the specific reason for the injury. The possibility that the hominid was butted by a large animal appears to be the most likely cause of the fracture.     

Prebiotic phosphate: a problem insoluble in water ? ]

It is well-known that in water phosphate readily reacts with calcium, precipitating as insoluble apatite. How phosphorus could have been available for prebiotic reactions is still an open problem. We suggest that phosphorus-containing compounds might have accumulated in a hydrophobic medium, since the absence of calcium ions would have prevented them from precipitating as apatite. Hydrophobic compounds may have been synthesized on the early Earth through the polymerization of methane or through Fischer-Tropsch-type reactions. Moreover, hydrophobic compounds would have been delivered to the early Earth by extraterrestrial infall. In previous articles (Morchio and Traverso [1999], Morchio et al. [2001]) we suggested that such hydrophobic material would have formed a hydrophobic layer on the surface of the sea, which would have provided an environment thermodynamically more suitable than water for the concentration and polymerization of organic molecules fundamental to life, particularly amino acids and (pyrimidine) bases. It may be hypothesized that elemental phosphorus or phosphorus-containing compounds (such as phosphite) deriving from volcanic eruptions would have ended up raining down into the hydrophobic layer, accumulating due to the absence of calcium ions, in an environment protected against hydrolysis. Phosphorus-containing compounds might have interacted with hydrophobic molecules in the layer giving rise to polymers. In particular, phosphite might have reacted with the hydrophobic amino acids, giving rise to phosphoamino acids, which, in turn, might have interacted with pyrimidine bases (relatively abundant in the layer) giving rise to peptides and oligonucleotide-like polymers. Indeed, it has been experimentally shown (Zhou et al. [1996]) that, in an anhydrous organic medium (pyridine), dialkilphosphite reacts with amino acids to form phosphoamino acids, which interact with pyrimidine nucleosides to give nucleotides, short oligonucleotides and phosphoryl peptides.