Detection of mutations in PCR products from clinical samples by surface plasmon resonance

Two different strategies for scanning and screening of mutations in polymerase chain reaction (PCR) products by hybridization analysis are described, employing real-time biospecific interaction analysis (BIA) for detection. Real-time BIA was used to detect differences in hybridization responses between PCR products and different 17-mer oligonucleotide probes. For the analysis using a biosensor instrument, two different experimental formats were investigated based on immobilization of either biotinylated PCR products or oligonucleotide probes onto a sensor chip. Applied on the human tumour suppressor p53 gene, differences in hybridization levels for full-match and mismatch situations employing both formats allowed the detection of point mutations in exon 6 PCR products, derived from a breast tumour biopsy sample. In addition, a mutant sample sequence could be detected in a 50/50 background of wild type exon 6 sequence. The suitability of the different formats for obtaining a regenerable system and a high throughput of samples is discussed. © 1997 John Wiley & Sons, Ltd.     

2,3,7,8-tetrachlorodibenzo-p-dioxin induces lecithin: retinol acyltransferase transcription in the rat kidney

Vitamin A (retinoids) has an essential role in development and throughout life of humans and animals. Consequently, effects of the environmental pollutant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on retinoid metabolism may be contributory to its toxicity. This study was performed to clarify the mechanism behind dioxin-induced retinyl ester formation in the rat kidney. In addition we investigated the possible role of CYP1A1 in dioxin-induced all-trans-retinoic acid (atRA) formation. Male Sprague-Dawley rats were exposed to a single oral dose of TCDD in a combined dose-response and time-course study, with doses ranging from 0.1 to 100 microg/kg bw and time points from 1 to 28 days. Levels of atRA and the expression of two potentially retinoic acid (RA)-controlled proteins critically involved in retinoid storage regulation, lecithin: retinol acyltransferase (LRAT) and cellular retinol binding protein I (CRBP I), were analyzed in liver and kidney. The expression and activity of cytochrome P4501A1 (assayed as ethoxyresorufin-O-deethylase activity) was assessed to gain insight into its potential role in RA synthesis. There was a significant increase in LRAT mRNA expression in the kidney, whereas no such increase could be observed in the liver, despite significantly increased atRA levels in both tissues. This suggests a tissue-specific regulation of LRAT by TCDD that may be dependent on other factors than atRA. Neither CRBP I mRNA nor protein levels were altered by TCDD. The time-course relationship between CYP1A1 activity and atRA levels in liver and kidney does not exclude a role of CYP1A1 in TCDD-induced RA synthesis. The observed altered regulation of the retinoid-metabolizing enzyme LRAT, together with the low doses and short time required by TCDD to change tissue RA levels, suggest that enzymes involved in retinoid metabolism are specific and/or direct targets of TCDD.     

Nitrogen mineralization and phenol accumulation along a fire chronosequence in northern Sweden

Scots pine (Pinus sylvestris L.) forests of northern Sweden are often considered to be N limited. This limitation may have been exacerbated by the elimination of wildfire as a natural disturbance factor in these boreal forests. Phenolic inhibition of N mineralization and nitrification (due to litter and exudates of ericaceous shrubs) has been proposed as a mechanism for N limitation of these forests, but this hypothesis remains largely untested. N mineralization rates, nitrification rates, and sorption of free phenolic compounds were assessed along a fire-induced chronosequence in northern Sweden. A total of 34 forest stands varying in age since the last fire were identified and characterized. Overstorey and understorey vegetative composition and depth of humus were analysed in replicated plots at all 34 sites. Eight of the forest stands aged 3-352 years since the last fire were selected for intensive investigation in which ten replicate ionic resin capsules (used to assess net N mineralization and nitrification) and non-ionic carbonaceous resin capsules (used to assess free phenolic compounds) were installed at the interface of humus and mineral soil. A highly significant correlation was observed between site age and net sorption of inorganic N to resin capsules. Net accumulation of NH₄⁺ and NO₃^- on resin capsules followed a linear decrease (R²=0.61, P<0.01) with time perhaps as a result of increased N immobilization with successional C loading. NO₃^- sorption to resin capsules followed a logarithmic decrease (R²=0.80, P<0.01) that may be related to a logarithmic increase in dwarf shrub cover and decreased soil charcoal sorption potential along this chronosequence. A replicated field study was conducted at one of the late successional field sites to assess the influence of charcoal and an added labile N source on N turnover. Three rates of charcoal (0, 100, and 1,000 g M^-2) and two rates of glycine (0 and 50 g N as glycine M^-2) were applied in a factorial design to microplots in a randomized complete block pattern. Net ammonification (as assessed by NH₄⁺ sorption to resins) was readily increased by the addition of a labile N source, but this increase in NH₄⁺ did not stimulate nitrification. Nitrification was stimulated slightly by the addition of charcoal resulting in similar levels of resin-sorbed NO₃^- as those found in early successional sites. Resin-sorbed polyphenol concentrations were decreased with charcoal amendments, but were actually increased with N amendments (likely due to decomposition of polyphenols). Net N mineralization appears to be limited by rapid NH₄⁺ immobilization whereas nitrification is limited by the lack of an appropriate environment or by the presence of inhibitory compounds in late successional forests of northern Sweden.     

The influence of spermine on the structural dynamics of yeast tRNAPhe

A tRNA^Phe derivative carrying ethidium at position 37 in the anticodon loop has been used to study the effect of spermine on conformational transitions of the tRNA. As previously reported (Ehrenberg, M., Rigler, R. and Wintermeyer, W. (1979) Biochemistry 18, 4588–4599) in the tRNA derivative the ethidium is present in three states (T₁–T₃) characterized by different fluorescence decay rates. T-jump experiments show two transitions between the states, a fast one (relaxation time 10–100 ms) between T₁ and T₂, and a slow one (100–1000 ms) between T₂ and T₃. In the presence of spermine the fast transition shows a negative temperature coefficient indicating the existence of a preequilibrium with a negative reaction enthalpy. Spermine shifts the distribution of states towards T₃, as does Mg²⁺, but the final ratio $\text{[}\text{T}{}_2\text{]}\text{[}\text{T}{}_1\text{]}$ obtained with spermine is higher than with Mg²⁺, which we tentatively interpret to mean that spermine stabilizes one particular conformation of the anticodon loop.     

Iodide transport in primary cultured thyroid follicle cells: evidence of a TSH-regulated channel mediating iodide efflux selectively across the apical domain of the plasma membrane.

The transport of iodide was studied in porcine thyroid follicle cells cultured in bicameral chambers. The continuous layer of polarized follicle cells, joined by tight junctions, formed a diffusion barrier between the two compartments (apical and basal) of the culture chamber. Uptake and efflux of 125I- at either surface (apical and basolateral) of the cells were thus possible to determine. Protein binding of iodide was inhibited by methimazole (10(-3) M) in all experiments. Radioiodide was taken up by the cells from the basal medium in a thyroid-stimulating hormone (TSH)-dose dependent manner with a maximal cell/medium ratio of 125I- of about 50 in cultures prestimulated with 0.1 to 1 mU/ml for 2 days. This uptake was inhibited by perchlorate and ouabain. In contrast, 125I- was not taken up from the apical medium. In preloaded cells, iodide efflux was rapidly (within 1-2 min) and dose-dependently (0.1-10 mU/ml) stimulated by TSH. Bidirectional measurements revealed that TSH stimulated iodide efflux in apical direction, leaving efflux in basal direction unchanged. In experiments with continuous uptake of label from the basal compartment, the TSH-stimulated efflux in apical direction had a duration of 4 to 6 min and resulted in a reduction in the cellular content of radioiodide by up to 80%. Decreased levels of cellular 125I- remained for at least 15 min after TSH addition. From our observations we conclude that the TSH-regulated uptake and efflux of iodide take place at opposite surfaces of the porcine thyroid follicle cell. Acutely stimulated iodide efflux is not the result of an increased permeability for iodide in the entire plasma membrane but only in the apical domain of this membrane. This implicates the presence of an iodide channel mediating TSH-stimulated efflux across the apical plasma membrane of the follicle cell. The mechanism is suggested to facilitate a vectorial transport of iodide in apical direction, i.e., to the lumen of the intact follicle.     

Studies in Montia L. and Claytonia L. and Allied Genera

The pollen morphology of several genera in Portulacaceae is described. Particular attention has been paid to the genera of the subfamily Montioideae, as a stage of continued monographical studies. Among genera especially dealt with are Claytonia, Montia, Crunocallis, Naiocrene, Neopaxia, Mona, Maxia, Limnalsine, and Montiastrum. In the taxonomical treatment of these genera the pollen morphology has proved to afford many important additional characters.

The pollen grains of Claytonia are distinguished from those of the remainder in being 3-colpate. The grains of the Claytonia-type have many similarities with those of Lewisia, a genus of the subfamily Portulacoideae. The other genera of Montioideae have pantocolpate pollen grains. Among these genera several different pollen types are distinguished, chiefly with regard to the sexine structures and the aperture membranes. The Montiastrum-type is especially interesting, with tholate grains, a particular pollen type not met with in any other genus in the family. The pollen morphology of some genera in the Portulacoideae is also treated. In some species in Calandrina and Talinum pantotreme pollen grains are observed with apertures transitional between pori and colpi. The apertures of the pantotreme grains are arranged in characteristic patterns.

Particular attention has been given to the variation of the pollen morphological characters. This variation has been examined with regard to the differences between different populations of the same species as well as between different species. The greatest variation has been observed in the shape and size of the grains. The structure and sculpture and thickness of the sexine and the aperture membranes are less variable. Some polyploid taxa are connected with the occurrence of pollen grains with divergent and varying aperture numbers.

In a survey of the genera the taxonomical results of the investigation are presented with particular regard to the pollen morphology. The new genus, Maxia Ö. Nilss., is described. One new species, Montia clara Ö. Nilss., is described and some new combinations are made.

Pollen morphological diagnoses are given for 46 different taxa. The aperture conditions for 96 different species are presented.     

Molecular Dynamics Study of Intrinsic Stability in Six RNA Terminal Loop Motifs

Abstract

Single stranded RNA molecules can assume a wide range of tertiary structures beyond the canonical A-form double helix. Certain sequences, termed motifs, are more common than a random distribution would suggest. The existence of such motifs can be rationalized in structural terms. In this study, we have investigated the intrinsic structural stability of RNA terminal loop motifs using multiple MD simulations in explicit water. Representative loops were chosen from the major tetraloop motifs, including also the U-turn motif. Not all loops retain their folded starting structure, but lowering the temperature to 277 K, or adding adjacent base pairs from the stem to which the motif is attached, helps stabilizing the folded loop structure.     

L-3-Phosphoglyceric acid,formed by ribulose-1,5-bisphosphate carboxylase,is the primary substrate for photorespiration: Experimental test of a hypothesis

Preparations of RuBP carboxylase are shown to carry out an oxygen dependent decarboxylation of L-3-phosphoglyceric acid. The product of this reaction is probably phosphoglycollate. L-3-phosphoglyceric acid, formed by RuBP carboxylase is therefore proposed to be the primary substrate for photorespiration.