Clustal W and Clustal X version 2.0

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/     

FTIR spectroscopy of NH3 on acidic and ionotropic alginate aerogels

The acidity of alginate aerogel films has been investigated by infrared spectroscopy of adsorbed NH(3). Supercritical drying of the alginate provided samples with a surface area of several hundred square meters per gram, in which the probe molecule could reach all acidic sites. Free carboxylic groups were studied on acid-gelled alginates and were found to behave as effective Br?nsted acid sites. Ionotropic alginate gels formed by alkaline earth cations presented only the Lewis acidity of the cations. Ionotropic gels formed by transition metal cations presented both Lewis and Br?nsted sites, because of the presence of a fraction of free carboxylic groups. The incomplete salification was correlated to the pH of the gelling solutions.     

Beshornin and beshornoside,steroidal saponins of Beshorneria yuccoides

Two new saponins beshornin and beshornoside have been isolated from the methanolic extract of Beshorneria yuccoides leaves and their structures elucidated. Beshornin is 3-O-[α-l-rhamnopyranosyl-(1 → 4)-β-d-glucopyranosyl- (1 → 2)-[α-l-rhamnopyranosyl-(1 -+ 4)-P-D-glucopyranosyl-(1 → 3)]-β-d-glucopyranosyl-(1 → 4)-β-d- galactopyranosyl-(25R)-5α-spirostan-3β-ol, whereas beshornoside is 3-O-[α-l-rhamnopyranosyl-(1 → 4)- β-d)-glycopyranosyl-(1 → 2)]-[α-l-rhamnopyranosyl-(1 → 4)-β-d-glucopyranosyl-(1 → 3)]-β-d-glucopyranosyl- (1 → 4)-β-d-galactopyranosyl 26-O-[β-d]-glucopyranosyl-(25R)-5α-furostan-3β,22α,26-triol.     

Short double-stranded RNA with immunostimulatory activity: sequence dependence

Small interfering RNAs (siRNA) are able to activate the mammalian innate immune system depending on their structure, sequence, and method of delivery. The immunostimulatory activity of double-stranded RNA can be applied to antiviral and antitumor therapy. Here we identified a set of 19-bp RNA duplexes with 3-nucleotid overhangs in the 3' ends that display immunostimulating activity (here and after immunostimulating RNA, or isRNA) and studied their sequence/activity relationships. It was found that the introduction of substitutions in the middle part of the isRNA sequence (10-16 positions counting from the 5' end of strand 1) does not alter the antiproliferative activity, while substitutions in the 3' end region of isRNA substantially reduce it. isRNAs efficiently inhibit the proliferation of human oral epidermoid carcinoma cells [half-maximal inhibitory concentration (IC(50)) values varied from 10 to 100 nM]. Our research demonstrated that antiproliferative effects of isRNAs are related to cell growth arrest, rather than the induction of apoptosis. These isRNAs strongly stimulate the synthesis of interferon-α (IFN-α), and to a lesser extent the synthesis of tumor necrosis factor (TNF-α) and interleukin-6 (IL-6), in adherent peripheral blood mononuclear cells. An intravenous injection of isRNA/Lipofectamine complexes into C57BL mice increases IFN-α and IL-6 levels in the blood serum up to 15-fold and 3-fold, respectively, compared to the control mice. The results obtained clearly demonstrate the pronounced immunostimulatory and antiproliferative properties of the isRNAs under study. Hence, these short double-stranded RNAs can be considered as potential agents for the therapy of oncological and viral diseases.     

Escape mechanisms after antiangiogenic treatment, or why are the tumors growing again?

Inhibitors of angiogenesis and radiation induce compensatory changes in the tumor vasculature both during and after cessation of treatment. In numerous preclinical studies, angiogenesis inhibitors were shown to be efficient in the treatment of many pathological conditions, including solid cancers. In most clinical trials, however, this approach turned out to have no significant effect, especially if applied as monotherapy. Recovery of tumors after therapy is a major problem in the management of cancer patients. The mechanisms underlying tumor recovery (or therapy resistance) have not yet been explicitly elucidated. This review deals with the transient switch from sprouting to intussusceptive angiogenesis, which may be an adaptive response of tumor vasculature to cancer therapy that allows the vasculature to maintain its functional properties. Potential candidates for molecular targeting of this angioadaptive mechanism are yet to be elucidated in order to improve the currently poor efficacy of contemporary antiangiogenic therapies.