Root production and turnover in an upland grassland subjected to artificial soil warming respond to radiation flux and nutrients, not temperature

Root demographic processes (birth and death) were measured using minirhizotrons in the soil warming experiments at the summit of Great Dun Fell, United Kingdom (845 m). The soil warming treatment raised soil temperature at 2 cm depth by nearly 3°C. The first experiment ran for 6 months (1994), the second for 18 (1995–1996). In both experiments, heating increased death rates for roots, but birth rates were not significantly increased in the first experiment. The lack of stimulation of death rate in 1996 is probably an artefact, caused by completion of measurements in late summer of 1996, before the seasonal demography was concluded: root death continued over the winter of 1995–1996. Measurements of instantaneous death rates confirmed this: they were accelerated by warming in the second experiment. In the one complete year (1995–1996) in which measurements were taken, net root numbers by the end of the year were not affected by soil warming. The best explanatory environmental variable for root birth rate in both experiments was photosynthetically active radiation (PAR) flux, averaged over the previous 5 (first experiment) or 10 days (second experiment). In the second experiment, the relationship between birth rate and PAR flux was steeper and stronger in heated than in unheated plots. Death rate was best explained by vegetation temperature. These results provide further evidence that root production acclimates to temperature and is driven by the availability of photosynthate. The stimulation of root growth due to soil warming was almost certainly the result of changes in nutrient availability following enhanced decomposition. Received: 4 May 1999 / Accepted: 18 May 1999     

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Background  

The human gastrointestinal (GI) tract contains a diverse collection of bacteria, most of which are unculturable by conventional microbiological methods. Increasingly molecular profiling techniques are being employed to examine this complex microbial community. The purpose of this study was to develop a microarray technique based on 16S ribosomal gene sequences for rapidly monitoring the microbial population of the GI tract.     

Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy

Scaffold or matrix-attachment regions (S/MARs) are thought to be involved in the organization of eukaryotic chromosomes and in the regulation of several DNA functions. Their characteristics are conserved between plants and humans, and a variety of biological activities have been associated with them. The identification of S/MARs within genomic sequences has proved to be unexpectedly difficult, as they do not appear to have consensus sequences or sequence motifs associated with them. We have shown that S/MARs do share a characteristic structural property, they have a markedly high predicted propensity to undergo strand separation when placed under negative superhelical tension. This result agrees with experimental observations, that S/MARs contain base-unpairing regions (BURs). Here, we perform a quantitative evaluation of the association between the ease of stress-induced DNA duplex destabilization (SIDD) and S/MAR binding activity. We first use synthetic oligomers to investigate how the arrangement of localized unpairing elements within a base-unpairing region affects S/MAR binding. The organizational properties found in this way are applied to the investigation of correlations between specific measures of stress-induced duplex destabilization and the binding properties of naturally occurring S/MARs. For this purpose, we analyze S/MAR and non-S/MAR elements that have been derived from the human genome or from the tobacco genome. We find that S/MARs exhibit long regions of extensive destabilization. Moreover, quantitative measures of the SIDD attributes of these fragments calculated under uniform conditions are found to correlate very highly (r2>0.8) with their experimentally measured S/MAR-binding strengths. These results suggest that duplex destabilization may be involved in the mechanisms by which S/MARs function. They suggest also that SIDD properties may be incorporated into an improved computational strategy to search genomic DNA sequences for sites having the necessary attributes to function as S/MARs, and even to estimate their relative binding strengths.