Nitrification by plants that also fix nitrogen

Nitrification is a key stage in the nitrogen cycle; it enables the transformation of nitrogen into an oxidized, inorganic state. The availability of nitrates produced by this process often limits primary productivity and is an important determinant in plant community ecology and biodiversity. Chemoautotrophic prokaryotes are recognized as the main facilitators of this process, although heterotrophic nitrification by fungi may be significant under certain conditions. However, there has been neither biochemical nor ecological evidence to support nitrification by photoautotrophic plants. Here we show how certain legumes that accumulate the toxin, 3-nitropropionic acid, generate oxidized inorganic nitrogen in their shoots, which is returned to the soil in their litter. In nitrogen-fixing populations this 'new' nitrate and nitrite can be derived from the assimilation of nitrogen gas. Normally, the transformation of elemental nitrogen from the atmosphere into a fixed oxidized form (as nitrate) is represented in the nitrogen cycle as a multiphasic process involving several different organisms. We show how this can occur in a single photoautotrophic organism, representing a previously undescribed feature of this biogeochemical cycle.     

Bottom water warming in the North Pacific Ocean

Observations of changes in the properties of ocean waters have been restricted to surface or intermediate-depth waters, because the detection of change in bottom water is extremely difficult owing to the small magnitude of the expected signals. Nevertheless, temporal changes in the properties of such deep waters across an ocean basin are of particular interest, as they can be used to constrain the transport of water at the bottom of the ocean and to detect changes in the global thermohaline circulation. Here we present a comparison of a trans-Pacific survey completed in 1985 (refs 4, 5) and its repetition in 1999 (ref. 6). We find that the deepest waters of the North Pacific Ocean have warmed significantly across the entire width of the ocean basin. Our observations imply that changes in water properties are now detectable in water masses that have long been insulated from heat exchange with the atmosphere.     

Resistance to mantle flow inferred from the electromagnetic strike of the Australian upper mantle

Seismic anisotropy is thought to result from the strain-induced lattice-preferred orientation of mantle minerals, especially olivine, owing to shear waves propagating faster along the a-axis of olivine crystals than along the other axes. This anisotropy results in birefringence, or 'shear-wave splitting', which has been investigated in numerous studies. Although olivine is also anisotropic with respect to electrical conductivity (with the a-axis being most conductive), few studies of the electrical anisotropy of the upper mantle have been undertaken, and these have been limited to relatively shallow depths in the lithospheric upper mantle. Theoretical models of mantle flow have been used to infer that, for progressive simple shear imparted by the motion of an overriding tectonic plate, the a-axes of olivine crystals should align themselves parallel to the direction of plate motion. Here, however, we show that a significant discrepancy exists between the electromagnetic strike of the mantle below Australia and the direction of present-day absolute plate motion. We infer from this discrepancy that the a-axes of olivine crystals are not aligned with the direction of the present-day plate motion of Australia, indicating resistance to deformation of the mantle by plate motion.     

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.     

Local protein-DNA interactions may determine nucleosome positions on yeast plasmids

The structure of the nucleosome core particle, the basic structural subunit of chromatin, is well known. Although nucleosomes often appear to be positioned randomly with respect to DNA sequences, in some cases they seem to occupy precisely defined positions on the DNA. The yeast plasmid TRP1ARS1 contains three precisely positioned, stable nucleosomes, I, II and III, which are flanked by nuclease-sensitive regions. Our aim in the present study was to determine whether the positions of these three nucleosomes relate to (1) protein-DNA interactions; (2) the limited space between nuclease-sensitive regions, which is just long enough to accommodate three yeast nucleosomes (that is, boundary conditions); or (3) proximity to the putative origin of replication in one of the nuclease-sensitive regions. We have tested these alternatives by analysing the positions of nucleosomes after insertion of various lengths of DNA into this region and assembly of chromatin in vivo. Our results suggest that specific protein-DNA interactions are the most likely determinants of these nucleosome positions.