Interruption of the fragile X syndrome expanded sequence d(CGG)(n) by interspersed d(AGG) trinucleotides diminishes the formation and stability of d(CGG)(n) tetrahelical structures

Fragile X syndrome is caused by expansion of a d(CGG) trinucleotide repeat sequence in the 5′ untranslated region of the first exon of the FMR1 gene. Repeat expansion is thought to be instigated by formation of d(CGG)_n secondary structures. Stable FMR1 d(CGG)_n runs in normal individuals consist of 6–52 d(CGG) repeats that are interrupted every 9–11 triplets by a single d(AGG) trinucleotide. By contrast, individuals having fragile X syndrome premutation or full mutation present >54–200 or >200–2000 monotonous d(CGG) repeats, respectively. Here we show that the presence of interspersed d(AGG) triplets diminished in vitro formation of bimolecular tetrahelical structures of d(CGG)₁₈ oligomers. Tetraplex structures formed by d(CGG)_n oligomers containing d(AGG) interspersions had lower thermal stability. In addition, tetraplex structures of d(CGG)₁₈ oligomers interspersed by d(AGG) triplets were unwound by human Werner syndrome DNA helicase at rates and to an extent that exceeded the unwinding of tetraplex form consisting of monotonous d(CGG)₁₈. Diminished formation and stability of tetraplex structures of d(AGG)-containing FMR1 d(CGG)_2–50 tracts might restrict their expansion in normal individuals.     

Human Ku antigen tightly binds and stabilizes a tetrahelical form of the Fragile X syndrome d(CGG)n expanded sequence

Hairpin and tetrahelical structures of a d(CGG)(n) sequence in the FMR1 gene have been implicated in its expansion in fragile X syndrome. The identification of tetraplex d(CGG)(n) destabilizing proteins (Fry, M., and Loeb, L. A.(1999) J. Biol. Chem. 274, 12797-12803; Weisman-Shomer, P., Naot, Y., and Fry, M. (2000) J. Biol. Chem. 275, 2231-2238) suggested that proteins might modulate d(CGG)(n) folding and aggregation. We assayed human TK-6 lymphoblastoid cell extracts for d(CGG)(8) oligomer binding proteins. The principal binding protein was identified as Ku antigen by its partial amino acid sequence and antigenicity. The purified 88/75-kDa heterodimeric Ku bound with similar affinities (K(d) approximately 1. 8-10.2 x 10(-9) mol/liter) to double-stranded d(CGG)(8).d(CCG)(8), hairpin d(CGG)(8), single-stranded d(CII)(8), or tetraplex structures of telomeric or IgG switch region sequences. However, Ku associated more tightly with bimolecular G'2 tetraplex d(CGG)(8) (K(d) approximately 0.35 x 10(-9) mol/liter). Binding to Ku protected G'2 d(CGG)(8) against nuclease digestion and impeded its unwinding by the tetraplex destabilizing protein qTBP42. Stabilization of d(CGG)(n) tetraplex domains in FMR1 by Ku or other proteins might promote d(CGG) expansion and FMR1 silencing.     

Characterization of a Helicobacter pylori vaccine candidate by proteome techniques

In a previous two-dimensional (2D) gel electrophoretic study of protein antigens of the gastric pathogen, Helicobacter pylori recognized by human sera, one of the highly and consistently reactive antigens, a protein with M_r of approximately 30?000 (Spot 15) seemed to be of special interest because of low yields on N-terminal protein sequencing. This suggested possible N-terminal modification, as the N-terminal sequence analysis of this 30?000 protein (Spot 15) did not provide a definitive match within the H. pylori genomic database. This protein was isolated by 2D polyacrylamide gel electrophoresis, evaluated by liquid chromatography–mass spectrometry, and found to consist of two related species of approximately 28?100 and 26?500. In parallel, the proteins within this spot were digested in situ with the endoprotease Lys-C. Analysis of the Lys-C digest by matrix-assisted laser desorption time-of-flight mass spectrometry, peptide mapping, and sequence analysis was conducted. Comparison of the mass and sequence of the Lys-C peptides with those derived from a H. pylori genomic library identified an open reading frame of approximately 300 base pairs as the source of the Spot 15 protein. This corresponded to HP0175 in the recently reported H. pylori genome sequence, an open reading frame with some homology to Campylobacter jejeuni cell binding protein 2. Mass spectral and sequence analysis indicated that Spot 15 was a processed product generated by proteolytic cleavage at both the carboxy and amino termini of the 34 open reading frame precursor.     

Occurrence of Colombian datura virus in the Terrestrial Orchid, Spiranthes cernua

Colombian datura virus was detected in the terrestrial orchid Spiranthes cernua using a combination of enzyme‐linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). The PCR strategy that we used to detect and confirm the identity of this virus has subsequently been used as a generalized procedure to confirm the identity of other potyviruses in ornamental species. This is the first report of this virus in an orchid and only the second report of a virus in this species.     

In vitro salt tolerance of cell wall enzymes from halophytes and glycophytes

The halophyte Suaeda maritima grows optimally in high concentrations(40–60% seawater) of salt. In these conditions the concentrationof salt in the apoplast of the leaves is at least 500 mM, aconcentration which severely inhibits the activity of cytoplasmicenzymes of both glycophytes and halophytes. The in vitro salttolerance of a number of cell wall enzymes was assayed in thepresence of a range of concentrations of NaCl. There was nosignificant inhibition of the activity of galactosidase, glucosidase,peroxidase or xyloglucan endo-transglycosylase extracted fromSuaeda maritima by in vitro concentrations of NaCl up to atleast 1 M. In vitro salt tolerance of cell wall enzymes wasnot restricted to the halophyte, similar enzymes from the non-halophilicrelative Kochia tricophylla, and from the glycophytes Vignaradiata and Cicer arietinum, were inhibited little, or not atall, by the same concentrations of salt. Pectin esterase wassomewhat less tolerant, but activity at 500 mM NaCl was stillgreater than at 0 mM NaCl in both Suaeda and Vigna. It is concludedthat these enzymes of the cell wall compartment are much moresalt-tolerant than cytoplasmic enzymes of higher plants. Theresults are discussed in relation to conditions thought to pertainin the apoplast. Key words: Apoplast, cell wall enzymes, halophyte, salt tolerance, Suaeda maritima     

Advantages of using different data sources in assessment of landscape change and its effect on visual scale

This paper presents a data-flexible indicator framework for analysis of visual landscape character; the VisuLands framework. The theory-based framework encompasses currently used indicators for visual assessment based on four different data sources: land cover data, aerial photographs, landscape photographs and field observations. This paper presents a study applying the VisuLands framework in analysis of landscape change and its effect on visual scale in a landscape in Southeast Sweden. The paper provides a critical assessment of the pros and cons of the approach. It identifies the advantages and disadvantages of using different data sources as well as the applicability and sensitivity of existing indicators in detecting visible landscape change. The results show that while some of the VisuLands indicators are relatively easily applied, others are more complex and demanding in terms of interpretation. The flexibility of the VisuLands framework makes it applicable and user-friendly as it helps meet the requirements and restrictions of the users. The assessment has shown that the different data sources complement each other and that applying indicators using various data sources, when available, will enhance the comprehensiveness of visual landscape assessment. The experience of this study is that the VisuLands framework is a useful tool in landscape analysis, monitoring and planning, which provides a repeatable, systematic and transparent approach with strong links to landscape theory.     

Protoplast isolation and culture from carob (Ceratonia siliqua) hypocotyls: ability of regenerated protoplasts to produce mannose-containing polysaccharides

The aim of this study was to isolate protoplasts from carob (Ceratonia siliqua L.) embryonic tissues with the ability to regenerate cell walls, divide and synthesize galactomannan, a valuable polysaccharide for industry. Protoplasts isolated from carob hypocotyl hooks regenerated cell walls within 24 h. The first divisions of the regenerated cells were observed after 2 days of culture. The highest percentage that successfully divided was achieved when the seedlings were grown under diffuse light, the hypocotyl hooks were plasmolysed for 1 h before incubation in the protoplast isolation solution and the protoplasts were cultured under diffuse light. After 9 days of culture, cell clusters, consisting of eight cells, had been produced, which underwent further mitotic divisions and which were expected to lead to callus formation. Polysaccharide and oligosaccharide synthesis during protoplast regeneration was studied by radiolabelling with exogenous d ‐[U‐¹⁴C]glucose, d ‐[U‐¹⁴C]mannose or d ‐[2‐³H]mannose, which gave rise to uniform, moderately specific and highly specific labelling, respectively. As revealed by the radioactivity distribution in cell wall monosaccharides, the regenerants deposited new wall polymers that differed markedly from those being synthesized by the hypocotyls from which the protoplasts had been isolated. The regenerants deposited large amounts of callose and smaller amounts of galactose‐, arabinose‐ and mannose‐containing polymers. The latter included glucuronomannan, as demonstrated by a new method involving partial acid hydrolysis followed by β‐glucuronidase (EC 3.2.1.31) digestion. The regenerating protoplasts also released soluble extracellular carbohydrates: polysaccharides which appeared to be mainly acidic arabinogalactans, and oligosaccharides which were mainly neutral and contained glucose, galactose and mannose. We conclude that regenerating carob protoplasts are a useful system for studying carbohydrate secretion, including mannose‐rich poly‐ and oligosaccharides.