Prenatal prediction of childhood-onset spinal muscular atrophy (SMA) in Turkish families

Childhood-onset spinal muscular atrophy (SMA) is one of the most common neurodegenerative genetic disorders. SMN1 is the SMA-determining gene deleted or mutated in the majority of SMA cases. There is no effective cure or treatment for this disease yet. Thus, the availability of prenatal testing is important. Here we report prenatal prediction for 68 fetuses in 63 Turkish SMA families using direct deletion analysis of the SMN1 gene by restriction digestion. The genotype of the index case was known in 40 families (Group A) but unknown in the remaining 23 families (Group B). A total of ten fetuses were predicted to be affected. Eight of these fetuses were derived from Group A and two of these fetuses were from Group B families. Two fetuses from the same family in Group A had the SMNhyb1 gene in addition to homozygous deletion of the NAIP gene. One fetus from Group A was homozygously deleted for only exon 8 of the SMN2 gene, and further analysis showed the presence of both the SMN1 and SMNhyb1 genes but not the SMN2 gene. In addition, one carrier with a homozygous deletion of only exon 8 of the SMN1 gene was detected to have a SMNhyb2 gene, which was also found in the fetus. To our knowledge, these are the first prenatal cases with SMNhyb genes. Follow-up studies demonstrated that the prenatal predictions and the phenotype of the fetuses correlated well in 33 type I pregnancies demonstrating that a careful molecular analysis of the SMN genes is very useful in predicting the phenotype of the fetus in families at risk for SMA. Copyright © 2002 John Wiley & Sons, Ltd.     

Vertical profiles of bacterial abundance,productivity and growth rates in coastal sediments of the central Great Barrier Reef lagoon

Vertical patterns of bacterial densities, productivity and specific growth rates in coastal muds, quartz sands and muddy sands of the central Great Barrier Reef lagoon were examined in summer (February) and autumn (May) 1988. Variations in these parameters with station location, sediment depth and season were complex, exhibiting significant main and interaction effects in most instances. Some trends were apparent despite the large and complex variations. Bacterial densities did not vary seasonally, ranging from 2.9 to 38.1×10⁹ cells g^-1 dry wt, averaged over sediment depth (0 to 20 cm) and seasons. Trend analysis revealed that densities decreased with increasing sediment depth. Bacterial production (tritiated thymidine incorporation into DNA) was high, ranging from 0.4 to 5.7 gCm^-2 d^-1 (integrated over 10 cm depth), as were specific growth rates (grand mean, =0.25 d^-1; range=0.004 to 1.3 d^-1). Both were generally higher in summer than in autumn. Vertical profiles of productivity and specific growth rates revealed actively growing bacterial assemblages down to 20 cm depth. Factors which may account for these very abundant and productive communities are: (1) subsurface accumulations of detritus exported from adjacent mangrove forests, and (2) physical disturbance from tidal scouring and severe climate (e.g. cyclones, wet-season floods). Disturbance events occur frequently enough to inhibit the development of highly sulphidic conditions, but stimulate production of bacterial types (aerobes, fermenters) capable of incorporating labelled thymidine into their DNA.     

Contribution of canopy leaching to sulphate deposition in a Scots pine forest

Radioactive sulphate (35SO4) was applied to the soil below a Scots pine forest on 23 June 1989, and its movement into the canopy and into throughfall and stemflow was measured over 4 months. The specific activity, Bq (mg S)(-1), of the canopy increased monotonically; uptake by current-year (1989) expanding needles was initially twice as fast as by older needles or live twigs. By 10 October the canopy average specific activity was 62 Bq (mg S)(-1). The specific activity of net throughfall (throughfall + stemflow - rain), deduced from measurements from six throughfall collectors, six stemflow collectors and two rain collectors, fell rapidly from 12.6 Bq (mg S)(-1) in late July to <1 Bq (mg S)(-1) in mid-August. The results suggest (assuming rapid equilibration of 35S with sulphate in soil) that root-derived sulphate contributed c. 3% of sulphate in net throughfall and that dry deposition of SO2 and sulphate particles contributed c. 97% of the 0.56 g S m(-2) measured in net throughfall over the period. Simultaneous measurements of SO2 at canopy height and of NH3 above and within the canopy gave mean concentrations of 5.9 and 0.86 microg m(-3), respectively, sufficient to account for the sulphate measured in net throughfall only if codeposition of NH3 and SO2 occurred to canopy surfaces. The large values of specific activity observed in July, however, indicate that throughfall composition may be closely related to recent soil input of sulphate, and that equilibrium cannot be safely assumed. The possibility of a significant contribution of soil-derived sulphate to sulphate deposition in net throughfall cannot be ruled out on the basis of this experiment.     

Modelling episodic acidification of surface waters: the state of science

Field studies of chemical changes in surface waters associated with rainfall and snowmelt events have provided evidence of episodic acidification of lakes and streams in Europe and North America. Modelling these chemical changes is particularly challenging because of the variability associated with hydrological transport and chemical transformation processes in catchments. This paper provides a review of mathematical models that have been applied to the problem of episodic acidification. Several empirical approaches, including regression models, mixing models and time series models, support a strong hydrological interpretation of episodic acidification. Regional application of several models has suggested that acidic episodes (in which the acid neutralizing capacity becomes negative) are relatively common in surface waters in several regions of the US that receive acid deposition. Results from physically based models have suggested a lack of understanding of hydrological flowpaths, hydraulic residence times and biogeochemical reactions, particularly those involving aluminum. The ability to better predict episodic chemical responses of surface waters is thus dependent upon elucidation of these and other physical and chemical processes.     

Effects of clearfelling on stream and soil water aluminium chemistry in three UK forests

Data are presented demonstrating how clearfelling has changed soil and stream water aluminium chemistry. For soil waters, a strong empirical relationship was observed between inorganic aluminium (Al(inorg)) and total inorganic anion (TIA) concentrations. Before felling, chloride and sulphate accounted for the largest proportion of the TIA concentration. After felling, in soils where nitrification was active, nitrate became increasingly important. Where this led to an increase in TIA, Al(inorg) concentrations increased. Over five years, nitrate concentrations have fallen, along with TIA, resulting in a sympathetic decline in Al(inorg). Streams draining clearfelled areas initially became more acid, although chloride and sulphate concentrations decreased. Stream water nitrate concentrations increased soon after felling and remained higher than controls for up to four years. While nitrate concentrations were high, Al(inorg) remained unchanged. Subsequently, as nitrate and TIA decreased, Al(inorg) also declined to concentrations below those in the control stream. Clearfelling upland forests will not necessarily result in immediate improvements in water quality, although long-term benefits may be seen before canopy-closure of the next crop.     

Trace metals in interstitial waters from sandstones: acidic inputs to shallow groundwaters

There is some evidence from southern Britain that shallow groundwaters in non-carbonate lithologies may be affected by acidic deposition. To investigate this, interstitial water profiles down to 12 m have been obtained from unsaturated sands or semi-consolidated sandstones from the Folkestone Beds (Lower Greensand) of Surrey and the Sherwood Sandstone of the West Midlands. The pH of the interstitial waters generally increased with depth and reflected an increase in the base saturation of the exchange complex. Beneath the highly acidic surface soil horizons (pH 3.0-3.5), interstitial waters with a pH of 4.0-4.5 were found down to depths of several metres. The pH progressively increased to around pH 5.5 because of base cation desorption and the weathering of silicate minerals. High concentrations of aluminium (10-20 mg litre(-1)) and other metals (Fe, Mn, Cu, Ni, Co, Zn, Be) were found in the interstitial water in the upper unsaturated zone. Most metal concentrations were strongly pH-dependent but also reflected the geochemical characteristics of the parent sands or sandstones. H+ and trace element concentrations were slightly higher beneath areas of afforestation than beneath heathland. The downward fluxes of solutes have been estimated using rainfall-derived chloride as a non-reactive solute. The profiles retain a record of 10-20 years input allowing the past inputs from SO4 and other species to be estimated using solute/chloride ratios. Cation exchange sites are probably depleted over a period of decades and there can be a significant decrease in the unsaturated zone pH as a result of increased or sustained acidic deposition. The shallow groundwater environment (0-15 m) in non-carbonate terrains is therefore a sensitive environment where high metal concentrations may be generated and may ultimately lead to water quality problems in shallow water supplies.