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A soluble agglutinin was purified by affinity chromatography of the celomic fluid of the marine worm Sipunculus nudus. This agglutinin requires metal cations for its activity and is specific for derivatives of D-galactose. It resulted lightly thermostable, with a pH optimum around 7.5. On SDSPAGE, it was resolved in two bands, of 33 and 31 kDa in reducing conditions and 29 and 26 kDa in non-reducing conditions. This behavior is probably due to the presence of disulfide bridges between cysteine residues, which are required for the correct functioning of the hemagglutinin, as β-mercaptoethanol completely abolish the agglutinating activity of cell-free celomic fluid. The purified lectin can influence in vitro phagocytosis of yeast by celomic leukocytes: in the presence of the molecule, ingestion of foreign particles results significantly decreased and yeast cells agglutinate and forms rosettes around the celomocytes. This suggests a role of the molecule in immunosurveillance. [ABSTRACT FROM AUTHOR]

Polynucleotide phosphorylase (PNPase), an enzyme conserved in bacteria and eukaryotic organelles, processively catalyzes the phosphorolysis of RNA, releasing nucleotide diphosphates, and the reverse polymerization reaction. In Escherichia coli, both reactions are implicated in RNA decay, as addition of either poly(A) or heteropolymeric tails targets RNA to degradation. PNPase may also be associated with the RNA degradosome, a heteromultimeric protein machine that can degrade highly structured RNA. Here, we report that ATP binds to PNPase and allosterically inhibits both its phosphorolytic and polymerization activities. Our data suggest that PNPase-dependent RNA tailing and degradation occur mainly at low ATP concentrations, whereas other enzymes may play a more significant role at high energy charge. These findings connect RNA turnover with the energy charge of the cell and highlight unforeseen metabolic roles of PNPase.

MIDAW (microarray data analysis web tool) is a web interface integrating a series of statistical algorithms that can be used for processing and interpretation of microarray data. MIDAW consists of two main sections: data normalization and data analysis. In the normalization phase the simultaneous processing of several experiments with background correction, global and local mean and variance normalization are carried out. The data analysis section allows graphical display of expression data for descriptive purposes, estimation of missing values, reduction of data dimension, discriminant analysis and identification of marker genes. The statistical results are organized in dynamic web pages and tables, where the transcript/gene probes contained in a specific microarray platform can be linked (according to user choice) to external databases (GenBank, Entrez Gene, UniGene). Tutorial files help the user throughout the statistical analysis to ensure that the forms are filled out correctly. MIDAW has been developed using Perl and PHP and it uses R/Bioconductor languages and routines. MIDAW is GPL licensed and freely accessible at http://muscle.cribi.unipd.it/midaw/. Perl and PHP source codes are available from the authors upon request.

Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats., Results: The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences., Availability: The program is freely available for non-profit organizations, upon request to the authors., Contact: giorgio.valle@unipd.it, Supplementary Information: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.