Synthesis of 2-Deoxy-4-thio-D-ribofuranose and Its 3-Azido Analogue from L-Arabinose; Intermediates in the Synthesis of 4′-Thiodeoxynucleosides

Abstract

1-O-Acetyl-3,5-di-O-benzoyl-2-deoxy-4-thio-α,β-D-ribofuranose and its 3-azido analogue have been prepared by an efficient route starting from L-arabinose. A key intermediate in this route is 2-deoxy-4,5-O-isopropylidene-L-erythro-pentose dibenzyl dithioacetal which is readily substituted in the 3-position thus offering extensive scope for the synthesis of 3-substituted 2-deoxy-4-thio-α,β-D-ribofuranoses and subsequent nucleoside derivatives.     

The role of saltwort (Batis maritima L.) in regeneration of degraded mangrove forests

While saltwort (Batis maritima L.) is common in the fringe mangrove forests of southwest Florida, its role in regeneration of degraded mangrove communities is not known. Given the potential encroachment and subsequent degradation of mangrove communities by sea-level rise, it is important to quantify the effect of early-colonizing vegetation to early mangrove seedling survival. A greater number of mangrove seedlings were observed in existing B. maritima patches compared to surrounding mudflats. A planting experiment was designed to determine whether B. maritima was responsible for the observed pattern. Black mangrove (Avicennia germinans L.) seedlings, raised in a nursery, were planted in previously established B. maritima patches and on mudflats with and without nursery-raised B. maritima. There was significantly lower mortality of A. germinans seedlings when planted in existing B. maritima patches (69%), compared to seedlings planted on the mudflats (93%), demonstrating that existing B. maritima improved A. germinans seedling survival. Nursery-raised B. maritima had lower mortality on open mudflats (28%), suggesting that it can tolerate conditions, which make it an early colonizer of newly available habitats. The primary mechanism proposed for improving seedling success is a slight increase in elevation provided by the dense root network of established B. maritima. These findings have implications for scientists and managers anticipating the response of mangroves to sea-level rise.     

Structure and activity of phosphoglycerate mutase

The structure of yeast phosphoglycerate mutase determined by X-ray crystallographic and amino acid sequence studies has been interpreted in terms of the chemical, kinetic and mechanistic observations made on this enzyme. There are two histidine residues at the active site, with imidazole groups almost parallel to each other and approximately 0.4 nm apart, positioned close to the 2 and 3 positions of the substrate. The simplest interpretation of the available information suggests that a ping-pong type mechanism operates in which at least one of these histidine residues participates in the phosphoryl transfer reaction. The flexible C-terminal region also plays an important role in the enzymic reaction.     

Haplotype analysis of phenylalanine hydroxylase alleles in polish families with phenylketonuria

Eight polymorphic restriction enzyme sites at phenylalanine hydroxylase locus from the parental chromosomes in Polish families with phenylketonuria were analyzed. Among 28 chromosomes studied, we identified haplotypes found within the Danish population. Haplotype 2 has been found in 25% of affected alleles. One of the patients studied is homozygous for this haplotype.     

Immunoelectrotransfer blot assay in acute and chronic human trichinellosis

An immunoelectrotransfer blot assay (IETB) using excretory secretory products of muscle larvae of Trichinella spiralis (ML-ESP) and the avidin biotin system was developed in order to characterize reactivity against ML-ESP in sera from patients with acute and chronic trichinellosis. A complete pattern of up to 13 bands was developed by sera from individuals with trichinellosis where doublets, triplets, or single bands were shown to have molecular weights of roughly 66, 55, 45, 36, 29, 24, and 14 kDa. The bands at approximately 55, 36, 29, and 14 kDa proved specific for T. spiralis. The band at approximately 55 kDa was present in all trichinellosis sera, whereas the approximately 14-kDa band was present in only a small percentage of sera. The development of approximately 36- and 29-kDa bands suggests a modulation of the reactivity against ML-ESP over time. IETB proved more sensitive for the population of chronic trichinellosis under study than a conventional diagnostic enzyme-linked immunosorbent assay, allowing negative or borderline serum samples to be determined. Thus, this technique, when applied for human trichinellosis surveillance, should provide a useful tool in endemic areas.     

Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences

MOTIVATION: The annotation of the Arabidopsis thaliana genome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use inside a computer-assisted annotation platform. We therefore need evaluation of prediction programs with Arabidopsis sequences containing multiple genes. RESULTS: We have developed AraSet, a data set of contigs of validated genes, enabling the evaluation of multi-gene models for the Arabidopsis genome. Besides conventional metrics to evaluate gene prediction at the site and the exon levels, new measures were introduced for the prediction at the protein sequence level as well as for the evaluation of gene models. This evaluation method is of general interest and could apply to any new gene prediction software and to any eukaryotic genome. The GeneMark.hmm program appears to be the most accurate software at all three levels for the Arabidopsis genomic sequences. Gene modeling could be further improved by combination of prediction software. AVAILABILITY: The AraSet sequence set, the Perl programs and complementary results and notes are available at http://sphinx.rug.ac.be:8080/biocomp/napav/. CONTACT: Pierre.Rouze@gengenp.rug.ac.be.