Linkage Disequilibrium Mapping of the Cornea Plana Congenita Gene CNA2

We recently assigned a gene for autosomal recessive cornea plana congenita (CNA2; MIM No. 217300) by linkage analysis to the approximately 3-cM interval between markers D12S82 and D12S327. Here, we extended these studies by exploiting the haplotype and linkage disequilibrium information that can be derived from the genetically isolated Finnish population and its subpopulations. By testing 32 independent families with 10 polymorphic markers in the CNA2 interval, strong allelic association between CNA2 and a set of markers with a peak at marker D12S351 was detected. Based on linkage disequilibrium analysis, the critical region for CNA2 could be narrowed to only 0.04-0.3 cM from marker D12S351, thus defining a critical interval 0.08-0.60 cM in length. These results provide a basis for highly focused positional cloning of CNA2.     

Maximum likelihood prediction of lake acidity based on sedimented diatoms

Abstract. As an example of ecological gradient analysis, Gaussian response functions, with Poisson or quasi-Poisson error distribution, were fitted for diatom taxa on a pH gradient. It is possible to predict or infer the pH of lake water from the fitted curves using the method of maximum likelihood, which is easily implemented in standard non-linear regressionprograms. Due to overdis-persion with respect to the Poisson distribution, moment estimates forthe negative binomial distribution were also applied, both in estimating the species response curves and in prediction. Simulations indicated that the theoretical maximum precision (measuredby standard deviation of prediction errors) in our data set was 0.17 pH units. The observed errors were much greater (SD 0.35 to 0.43). It seems that roughly equal proportions of the excess error were caused (1) by systematic differences between the training (estimation) data and the validation (prediction) data, and (2) from a misspecified model. It is suggested that the error due to model misspecification consists of inadequacy of the presumed error distribution and of inadequacy of the simple Gaussian response function.     

Nitrification and nitrous oxide production potentials in aerobic soil samples from the soil profile of a Finnish coniferous site receiving high ammonium deposition

Abstract Using aerobic soil slurry technique nitrification and nitrous oxide production were studied in samples from a pine site in Western Finland. The site received atmospheric ammonium deposition of 7–33 kg N ha⁻¹ a⁻¹ from a mink farm. The experiments with soil slurries showed that the nitrification potential in the litter layer was higher at pH 6 than at pH 4. However, the nitrification potentials in the samples from the organic and mineral horizons at pH 6 and 4 were almost equal. Also N₂O was produced at a higher rate at pH 6 than at pH 4 in slurries of the litter layer samples. The reverse was true for samples from the organic and mineral horizons. The highest N₂O production and nitrification rates were measured in the suspensions of litter layer samples. Nitrification activity in field-moist soil samples was lower than the activity in the slurries indicating that the availability of ammonium limited nitrification in these soils. Acetylene (2.5 kPa) retarded nitrification activity (70-–100%) and N₂O production (40 – 90%) in soil slurries. Acetylene inhibited the N₂O production by 40–60% during the first 3 days after its addition to field-moist samples incubated in aerobic atmosphere. After 3 days the inhibition became much lower (4–5%). The results indicate that, in soil profiles of boreal coniferous forests receiving ammonium deposition, chemolithotrophic nitrification may have importance in the N₂O production, and that changes in soil pH affect differently nitrification as well as N₂O production in litter and deeper soil layers.     

Reconstruction of the carbon balance for microsites in a boreal oligotrophic pine fen, Finland

 Carbon dioxide (CO₂) exchange was studied at flark (minerotrophic hollow), lawn and hummock microsites in an oligotrophic boreal pine fen. Statistical response functions were constructed for the microsites in order to reconstruct the annual CO₂ exchange balance from climate data. Carbon accumulation was estimated from the annual net CO₂ exchange, methane (CH₄) emissions and leaching of carbon. Due to high water tables in the year 1993, the average carbon accumulation at the flark, Eriophorum lawn, Carex lawn and hummock microsites was high, 2.91, 6.08, 2.83 and 2.66 mol C m^–2, respectively, and for the whole peatland it was 5.66 mol m^–2 year^–1. During the maximum primary production period in midsummer, hummocks with low water tables emitted less methane than predicted from the average net ecosystem exchange (NEE), while the Carex lawns emitted slightly more. CH₄ release during that period corresponded to 16% of the contemporary NEE. Annual C accumulation rate did not correlate with annual CH₄ release in the microsites studied, but the total community CO₂ release seemed to be related to CH₄ emissions in the wet microsites, again excluding the hummocks. The dependence of CO₂ exchange dynamics on weather events suggests that daily balances in C accumulation are labile and can change from net carbon uptake to net release, primarily in high hummocks on fens under warmer, drier climatic conditions. Received: 16 August 1996 / Accepted: 30 November 1996     

Alternative splicing of human and mouse NPFF2 receptor genes: Implications to receptor expression

Alternative splicing has an important role in the tissue-specific regulation of gene expression. Here we report that similar to the human NPFF2 receptor, the mouse NPFF2 receptor is alternatively spliced. In human the presence of three alternatively spliced receptor variants were verified, whereas two NPFF2 receptor variants were identified in mouse. The alternative splicing affected the 5′ untranslated region of the mouse receptor and the variants in mouse were differently distributed. The mouse NPFF system may also have species-specific features since the NPFF2 receptor mRNA expression differs from that reported for rat.     

Survival of Mycobacterium avium in Drinking Water Biofilms as Affected by Water Flow Velocity, Availability of Phosphorus, and Temperature

Mycobacterium avium is a potential pathogen occurring in drinking water systems. It is a slowly growing bacterium producing a thick cell wall containing mycolic acids, and it is known to resist chlorine better than many other microbes. Several studies have shown that pathogenic bacteria survive better in biofilms than in water. By using Propella biofilm reactors, we studied how factors generally influencing the growth of biofilms (flow rate, phosphorus concentration, and temperature) influence the survival of M. avium in drinking water biofilms. The growth of biofilms was followed by culture and DAPI (4′,6′-diamidino-2-phenylindole) staining, and concentrations of M. avium were determined by culture and fluorescence in situ hybridization methods. The spiked M. avium survived in biofilms for the 4-week study period without a dramatic decline in concentration. The addition of phosphorus (10 μg/liter) increased the number of heterotrophic bacteria in biofilms but decreased the culturability of M. avium. The reason for this result is probably that phosphorus increased competition with other microbes. An increase in flow velocity had no effect on the survival of M. avium, although it increased the growth of biofilms. A higher temperature (20°C versus 7°C) increased both the number of heterotrophic bacteria and the survival of M. avium in biofilms. In conclusion, the results show that in terms of affecting the survival of slowly growing M. avium in biofilms, temperature is a more important factor than the availability of nutrients like phosphorus.