The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments

How to sample alignments from their posterior probability distribution given two strings is shown. This is extended to sampling alignments of more than two strings. The result is first applied to the estimation of the edges of a given evolutionary tree over several strings. Second, when used in conjunction with simulated annealing, it gives a stochastic search method for an optimal multiple alignment.Correspondence to: L. Allison     

Nucleotide sequence and expression of a ripening and water stress-related cDNA from tomato with homology to the MIP class of membrane channel proteins

The nucleotide sequence and derived amino acid sequence were determined for a full-length version of the tomato cDNA clone, pTOM75, the mRNA for which has previously been shown to accumulate in roots, ripening fruit and senescing leaves. Computer analysis of the predicted protein product, which we have named tomato ripening-associated membrane protein (TRAMP) indicates strong homology to known transmembrane channel proteins from other organisms. Northern analysis showed that this gene was induced by waterstress and that this induction was unaffected in an ABA-deficient genetic back-ground.     

A linkage study in seven breast cancer families.

Seven breast cancer families are examined for evidence of linkage to a site in the region of 17q12-q21, by using five markers. The families constitute a subset of a larger series of familial breast cancer; the seven families were selected because constitutional DNA was available on informative members, either from clinical samples or extracted from paraffin blocks. Two-point lod scores are reported. The maximum lod score, 0.8824, is obtained with marker NM23 at theta = 0. This is clearly not significant in itself; however, when taken in context with evidence from existing reports, it provides support for linkage to this region.     

mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans.

The mtDNA variation of 411 individuals from 10 aboriginal Siberian populations was analyzed in an effort to delineate the relationships between Siberian and Native American populations. All mtDNAs were characterized by PCR amplification and restriction analysis, and a subset of them was characterized by control region sequencing. The resulting data were then compiled with previous mtDNA data from Native Americans and Asians and were used for phylogenetic analyses and sequence divergence estimations. Aboriginal Siberian populations exhibited mtDNAs from three (A, C, and D) of the four haplogroups observed in Native Americans. However, none of the Siberian populations showed mtDNAs from the fourth haplogroup, group B. The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas. Our findings support the hypothesis that the first humans to move from Siberia to the Americas carried with them a limited number of founding mtDNAs and that the initial migration occurred between 17,000-34,000 years before present.     

Presence of anisotropic (birefringent) crystalline structures in embryonic and juvenile monogonont rotifers

A systematic survey for the presence of birefringent (anisotropic) structures in rotifers was undertaken. Several common features of rotifers exhibit anisotropism (e.g. trophi & muscles). However, unusual anisotropic crystalline structures (ACS) were found in late stage embryos (i.e. possessing eyespots and trophi, and showing movement). ACS were found in 18 of 26 species of monogonont rotifers (comprising 11 genera of 5 families). In Sinantherina socialis, ACS were present in the lower gut as compact, spherical masses of minute crystals that slowly broke apart and disappeared within 20 hours of hatching. Although several authors have described the existence of refractive bodies in rotifers, to my knowledge this is the first report of their birefringent properties.     

Regional differences in glutaminase activation by phosphate and calcium in rat brain: Impairment in aged rats and implications for regional glutaminase isozymes

Regional regulation of glutaminase by phosphate and calcium was examined in the temporal cortex (TCX), striatum (STR) and hippocampus (HIPP) from adult and aged male F344 rats. Phosphate-dependent glutaminase activity in adult rats was significantly lower (35–43%) in the HIPP (100 and 150 mM) and STR (150 mM) compared to PAG activity in the TCX. Phosphate activation in aged rats was 50–60% lower in the HIPP at concentrations greater than 25 mM compared to the aged TCX or STR. PAG activity in the TCX and STR was unaffected by age, but was significantly reduced (30–50%) in the HIPP from aged rats at phosphate concentrations of 25 mM and greater when compared to adult rats. In adult rats at concentrations of CaCl₂ above 1 mM, PAG activity was significantly lower (60–75%) in the STR and HIPP when compared to the TCX. In aged rats, PAG activity (1 mM CaCl₂) in the HIPP was significantly less (50%) than STR PAG activity in aged rats. Diminished PAG activity was seen only in the TCX (2.5 mM; 32%), and the HIPP (0.5 mM; 25% and 1 mM; 38%) at higher calcium concentrations compared to adult. Phosphate-independent calcium activation of PAG occurred in the HIPP but not in either the TCX or the STR. Addition of phosphate resulted in a synergistic activation of PAG in the STR and TCX, but not in the HIPP. These findings suggest that PAG is regionally regulated by phosphate and calcium, and this regulation is impaired in aged rats. These data also support the hypothesis that isozymes of PAG exist with different regulatory properties.Abbreviation PAG Phosphate-activated glutaminase - L-glutamine amidohydrolase EC 3.5.1.2 - TCX temporal cortex - STR striatum - HIPP hippocampus - F344 Fischer-344 rat