Saikosaponin-d,a novel SERCA inhibitor,induces autophagic cell death in apoptosis-defective cells

Autophagy is an important cellular process that controls cells in a normal homeostatic state by recycling nutrients to maintain cellular energy levels for cell survival via the turnover of proteins and damaged organelles. However, persistent activation of autophagy can lead to excessive depletion of cellular organelles and essential proteins, leading to caspase-independent autophagic cell death. As such, inducing cell death through this autophagic mechanism could be an alternative approach to the treatment of cancers. Recently, we have identified a novel autophagic inducer, saikosaponin-d (Ssd), from a medicinal plant that induces autophagy in various types of cancer cells through the formation of autophagosomes as measured by GFP-LC3 puncta formation. By computational virtual docking analysis, biochemical assays and advanced live-cell imaging techniques, Ssd was shown to increase cytosolic calcium level via direct inhibition of sarcoplasmic/endoplasmic reticulum Ca²⁺ ATPase pump, leading to autophagy induction through the activation of the Ca²⁺/calmodulin-dependent kinase kinase–AMP-activated protein kinase–mammalian target of rapamycin pathway. In addition, Ssd treatment causes the disruption of calcium homeostasis, which induces endoplasmic reticulum stress as well as the unfolded protein responses pathway. Ssd also proved to be a potent cytotoxic agent in apoptosis-defective or apoptosis-resistant mouse embryonic fibroblast cells, which either lack caspases 3, 7 or 8 or had the Bax-Bak double knockout. These results provide a detailed understanding of the mechanism of action of Ssd, as a novel autophagic inducer, which has the potential of being developed into an anti-cancer agent for targeting apoptosis-resistant cancer cells.     

Structure-based library design and the discovery of a potent and selective mast cell β-tryptase inhibitor as an oral therapeutic agent

A solid phase combinatorial library was designed based on X-ray structures and in-silico models to explore an inducible S4+ pocket, which is formed by a simple side-chain rotation of Tyr95. This inducible S4+ pocket is unique to β-tryptase and does not exist for other trypsin-like serine proteases of interest. Therefore, inhibitors utilizing this pocket have inherent advantages for being selective against other proteases in the same family. A member of this library was found to be a potent and selective β-tryptase inhibitor with a suitable pharmacokinetic profile for further clinical evaluation.     

St John's wort for depression--an overview and meta-analysis of randomised clinical trials.

OBJECTIVE--To investigate if extracts of Hypericum perforatum (St John''s wort) are more effective than placebo in the treatment of depression, are as effective as standard antidepressive treatment, and have fewer side effects than standard antidepressant drugs. DESIGN--Systematic review and meta-analysis of trials revealed by searches. TRIALS--23 randomised trials including a total of 1757 outpatients with mainly mild or moderately severe depressive disorders: 15 (14 testing single preparations and one a combination with other plant extracts) were placebo controlled, and eight (six testing single preparations and two combinations) compared hypericum with another drug treatment. MAIN OUTCOME MEASURES--A pooled estimate of the responder rate ratio (responder rate in treatment group/responder rate in control group), and numbers of patients reporting and dropping out for side effects. RESULTS--Hypericum extracts were significantly superior to placebo (ratio = 2.67; 95% confidence interval 1.78 to 4.01) and similarly effective as standard antidepressants (single preparations 1.10; 0.93 to 1.31, combinations 1.52; 0.78 to 2.94). There were two (0.8%) drop outs for side effects with hypericum and seven (3.0%) with standard antidepressant drugs. Side effects occurred in 50 (19.8%) patients on hypericum and 84 (52.8%) patients on standard antidepressants. CONCLUSION--There is evidence that extracts of hypericum are more effective than placebo for the treatment of mild to moderately severe depressive disorders. Further studies comparing extracts with standard antidepressants in well defined groups of patients and comparing different extracts and doses are needed.     

Lung uptake of antibodies to endothelial antigens: key determinants of vascular immunotargeting

Vascular immunotargeting is a mean for a site-selective delivery of drugs and genes to endothelium. In this study, we compared recognition of pulmonary and systemic vessels in rats by candidate carrier monoclonal antibodies (MAbs) to endothelial antigens platelet endothelial cell adhesion molecule (PECAM)-1 (CD31), intercellular adhesion molecule (ICAM)-1 (CD54), Thy-1.1 (CD90.1), angiotensin-converting enzyme (ACE; CD143), and OX-43. Tissue immunostaining showed that endothelial cells were Thy-1.1 positive in capillaries but negative in large vessels. In the lung, anti-ACE MAb provided a positive staining in 100% capillaries vs. 5-20% capillaries in other organs. Other MAbs did not discriminate between pulmonary and systemic vessels. We determined tissue uptake after infusion of 1 microg of (125)I-labeled MAbs in isolated perfused lungs (IPL) or intravenously in intact rats. Uptake in IPL attained 46% of the injected dose (ID) of anti-Thy-1.1 and 20-25% ID of anti-ACE, anti-ICAM-1, and anti-OX-43 (vs. 0.5% ID of control IgG). However, after systemic injection at this dose, only anti-ACE MAb 9B9 displayed selective pulmonary uptake (16 vs. 1% ID/g in other organs). Anti-OX-43 displayed low pulmonary (0.5% ID/g) but significant splenic and cardiac uptake (7 and 2% ID/g). Anti-Thy-1.1 and anti-ICAM-1 displayed moderate pulmonary (4 and 6% ID/g, respectively) and high splenic and hepatic uptake (e.g., 18% ID/g of anti-Thy-1.1 in spleen). The lung-to-blood ratio was 5, 10, and 15 for anti-Thy-1.1, anti-ACE, and anti-ICAM-1, respectively. PECAM antibodies displayed low pulmonary uptake in perfusion (2% ID) and in vivo (3-4% ID/g). However, conjugation with streptavidin (SA) markedly augmented pulmonary uptake of anti-PECAM in perfusion (10-54% ID, depending on an antibody clone) and in vivo (up to 15% ID/g). Therefore, ACE-, Thy-1.1-, ICAM-1-, and SA-conjugated PECAM MAbs are candidate carriers for pulmonary targeting. ACE MAb offers a high selectivity of pulmonary targeting in vivo, likely because of a high content of ACE-positive capillaries in the lungs.     

Evaluation of the impact of recreational dive activity on the community structure of some coral reefs at Los Roques Archipelago National Park, Venezula

In order to evaluate if snorkeling had significant effects on coral community structure, three different coral reefs (Madrizquí, Pelona de Rabusquí and Crasquí) located at Archipelago Los Roques National Park, Venezuela, were surveyed. For each site, the coral community structure of two different areas, one subjected to intense snorkeling use (FB) and other not frequently used (PFB), were compared. Community structure was determined with 1 m2-quadrants and 20 m-long transects. These communities were described in terms of species richness, diversity (Shannon-Wiener) and evenness indexes, live and dead coral cover and cover of other organisms (sponges, octocorals and algae). Comparisons within sites were performed with a Kruskall-Wallis test. A total of 24 species of scleractinian corals were found. Live coral cover ranged from 29.9% +/- 26.43 (Crasquí) to 34.55% +/- 6.43 (Madrizquí), while dead coral cover ranged from 32.51% +/- 2.86 (Madrizquí) to 60.78% +/- 21.3 (Pelona de Rabusquí). The PFB areas showed higher live coral cover compared to FB areas; however, significant differences were only found in Crasquí and Pelona de Rabusquí (p < 0.05). Species richness, diversity and evenness were variable and no trends were observed between FB and PFB areas. The frequency of both damaged and diseased colonies were low (< 1%), most damages observed were natural (parrotfish predation). Damages caused by divers such as fin impacts, were not found at the reefs studied. These results suggest that, currently, diving pressure is not as high to cause massive loses of live coral cover in these reefs. However, the lack of strict controls for these activities might produce long-term changes in the structure of these coral communities.     

Present state of diseases and other signs of reef deterioration at seven coral reefs at Los Roques Archipelago National Park, Venezuela

This work was aimed to determine the incidence of coral diseases in six different reef sites at the Parque Nacional Archipiélago de Los Roques, Venezuela: Arrecife de herradura, Arrecife costanero, both at Dos Mosquises Sur Key, Boca de Cote, Carenero, Crasquí and Pelona de Rabusquí. Each reef was surveyed by using ten 10 m2-band transects (10 x 1 m), placed parallel to the long axis of the reef within a depth gradient ranging from 1 to 9 m depth. All healthy and injured corals, along each band transect, were counted and identified to species level. Additionally, all diseases and recent mortality that were still identifiable on each colony were also recorded. The occurrence of diseased colonies and other signs of reef decline between localities were compared by means of a Chi2 test. The absolute, relative and mean incidence was estimated for each disease and other signs of damage observed for all coral species surveyed at each site. The overall incidence of coral diseases was low for all the localities surveyed, only 6.04% of the 3 344 colonies observed, showed signs of diseases. The most important diseases recorded were the Yellow-Blotch Disease (YBD) and Dark Spots Disease (DSD) with 2.1% +/- 1.52 y 2.1% +/- 2.54, respectively. Significant differences were found in the incidence of coral diseases between reef sites (Chi2 p < 0.05). Finally, the occurrence of colonies injured by parrotfish bites and pomacentrids was higher compared with the incidence of coral diseases for all the reefs surveyed. In conclusion, currently the proportion of healthy colonies at Los Roques coral reefs is higher than the percentage of both diseased and injured colonies.     

Chromosome 6p influences on different dyslexia-related cognitive processes: further confirmation

In this study, which is a continuation and an extension of an earlier study, we enrolled two new families (N=31) and recruited more individuals from the previously ascertained families (N=56). The eight multiplex families (N=171) presented in this study were ascertained from a sample of adult probands whose childhood reading history is well documented through archival information. Six phenotypes were constructed to span a range of dyslexia-related cognitive processes. These phenotypes were (1) phonemic awareness (of spoken words); (2) phonological decoding (of printed nonwords); (3) rapid automatized naming (of colored squares or object drawings); (4) single-word reading (orally, of printed real words); (5) vocabulary; and (6) spelling (of dictated words). In addition, the diagnosis of lifelong dyslexia was established by clinical means. Genotyping was done with nine highly polymorphic markers from the 6p22.3-6p21.3 region. The results of two- and multipoint identity-by-descent and identity-by-state analyses supported the importance of a putative locus in the D6S464-D6S273 region for a number of dyslexia-related cognitive deficits.     

Partition decoupling for multi-gene analysis of gene expression profiling data

Background

Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conformations is generally done clustering the large ensemble of structures that are generated. Recently, Self-Organising Maps (SOMs) were reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data mining problems. We present a novel strategy to analyse and compare conformational ensembles of protein domains using a two-level approach that combines SOMs and hierarchical clustering.

Results

The conformational dynamics of the α-spectrin SH3 protein domain and six single mutants were analysed by MD simulations. The Cα's Cartesian coordinates of conformations sampled in the essential space were used as input data vectors for SOM training, then complete linkage clustering was performed on the SOM prototype vectors. A specific protocol to optimize a SOM for structural ensembles was proposed: the optimal SOM was selected by means of a Taguchi experimental design plan applied to different data sets, and the optimal sampling rate of the MD trajectory was selected. The proposed two-level approach was applied to single trajectories of the SH3 domain independently as well as to groups of them at the same time. The results demonstrated the potential of this approach in the analysis of large ensembles of molecular structures: the possibility of producing a topological mapping of the conformational space in a simple 2D visualisation, as well as of effectively highlighting differences in the conformational dynamics directly related to biological functions.

Conclusions

The use of a two-level approach combining SOMs and hierarchical clustering for conformational analysis of structural ensembles of proteins was proposed. It can easily be extended to other study cases and to conformational ensembles from other sources.     

Effects of tissue culture on a highly repetitive DNA sequence (E180 satellite) in Medicago sativa

Genomic DNA extracted from leaves of sixteen alfalfa genotypes, six-week-old callus cultures derived from them and from a suspension culture was used in Southern blots and slot blots probed with alfalfa E180 satellite DNA. The restriction patterns revealed by the E180 probe did not differ among alfalfa genotypes and no differences between the leaf and callus restriction patterns were seen. However, the number of copies of the E180 satellite was lower in the callus samples than in the corresponding leaf samples and significant differences in copy number among callus samples were detected. Genomic stress induced by tissue culture may have caused the reduction in copy number. This phenomenon may be important in the generation of somaclonal variation in alfalfa.