Dark and Photometabolism of Sugars by a Blue Green Alga: Tolypothrix tenuis

The carbohydrate metabolism of the autotrophically grown blue-green alga, Tolypothrix tenuis, was studied. The alga respires glucose, fructose, galactose, and ribose.     

Bak Foong protects dopaminergic neurons against MPTP-induced neurotoxicity by its anti-apoptotic activity

Bak Foong pill (BFP) is a well-known traditional Chinese medicine used for treatment of various gynaecological disorders. In addition, it exerts beneficial effects on other functional systems including the central nervous system. In the present study, we have investigated the possible neuroprotective action of BFP upon the nigrostriatal dopaminergic system by examining its effect on the expression patterns of tyrosine hydroxylase (TH) and dopamine transporter (DAT) in the 1-methyl-4-phenyl-1,2,3,6-tetrahyrdropyridine (MPTP)-induced Parkinson's disease (PD) mouse model. MPTP significantly decreased TH and DAT mRNA levels in the striatum and midbrain of both female and male C57BL/6 mice. However, with BFP pre-treatment mice showed a reduced neurotoxicity, with TH and DAT mRNA levels either not affected by MPTP or affected to a lesser extent in the midbrain and striatum when compared to vehicle treated animals. Possible anti-apoptotic activity of BFP was further studied in a dopamine-secreting neuroendocrine cell line, PC12. In this assay, MPTP elevated the expression of a pro-apoptotic gene, Bax, while this expression was reduced by BFP pre-treatment. Flow cytometry results also revealed that the effect of MPTP-induced apoptosis in PC12 cell lines was significantly reduced by BFP. The present results suggest that BFP is able to protect dopaminergic neurons from neurotoxin-induced neuronal injury with anti-apoptotic activity being one of the possible mechanisms.     

Differential regulation of nuclear and mitochondrial Bcl-2 in T cell apoptosis

Activated T cells require anti-apoptotic cytokines for their survival. The anti-apoptotic effects of these factors are mediated by their influence on the balance of expression and localisation of pro- and anti-apoptotic members of the Bcl-2 family. Among the anti-apoptotic Bcl-2 family members, the expression level of Bcl-2 itself and its interaction with the pro-apoptotic protein Bim are now regarded as crucial for the regulation of survival in activated T cells. We studied the changes in Bcl-2 levels and its subcellular distribution in relation to mitochondrial depolarisation and caspase activation in survival factor deprived T cells. Intriguingly, the total Bcl-2 level appeared to remain stable, even after caspase 3 activation indicated entry into the execution phase of apoptosis. However, cell fractionation experiments showed that while the dominant nuclear pool of Bcl-2 remained stable during apoptosis, the level of the smaller mitochondrial pool was rapidly downregulated. Signals induced by anti-apoptotic cytokines continuously replenish the mitochondrial pool, but nuclear Bcl-2 is independent of such signals. Mitochondrial Bcl-2 is lost rapidly by a caspase independent mechanism in the absence of survival factors, in contrast only a small proportion of the nuclear pool of Bcl-2 is lost during the execution phase and this loss is a caspase dependent process. We conclude that these two intracellular pools of Bcl-2 are regulated through different mechanisms and only the cytokine-mediated regulation of the mitochondrial pool is relevant to the control of the initiation of apoptosis. D. Scheel-Toellner and K. Raza have contributed equally to this study.     

Inhibition of cyclooxygenase-1 lowers proliferation and induces macroautophagy in colon cancer cells

Evolving evidence supports that cyclooxygenase-1 (COX-1) takes part in colon carcinogenesis. The effects of COX-1 inhibition on colon cancer cells, however, remains obscured. In this study, we demonstrate that COX-1 inhibitor sc-560 inhibited colon cancer cell proliferation with concomitant G₀/G₁-phase cell cycle arrest. The anti-proliferative effect was associated with down-regulation of c-Fos, cyclin E₂ and E₂F-1 and up-regulation of p21^Waf1/Cip1 and p27^Kip1. In addition, sc-560 induced macroautophagy, an emerging mechanism of tumor suppression, as evidenced by the formation of LC3⁺ autophagic vacuoles, enhanced LC3 processing, and the accumulation of acidic vesicular organelles and autolysosomes. In this connection, 3-methyladenine, a Class III phosphoinositide 3-kinase inhibitor, significantly abolished the formation of LC3⁺ autophagic vacuoles and the processing of LC3 induced by sc-560. To conclude, this study reveals the unreported relationship between COX-1 and proliferation/macroautophagy of colon cancer cells.     

TiLIA: a software package for image analysis of firefly flash patterns

As flash signaling patterns of fireflies are species specific, signal‐pattern analysis is important for understanding this system of communication. Here, we present time‐lapse image analysis (TiLIA), a free open‐source software package for signal and flight pattern analyses of fireflies that uses video‐recorded image data. TiLIA enables flight path tracing of individual fireflies and provides frame‐by‐frame coordinates and light intensity data. As an example of TiLIA capabilities, we demonstrate flash pattern analysis of the fireflies Luciola cruciata and L. lateralis during courtship behavior.     

A unified solution for different scenarios of predicting drug-target interactions via triple matrix factorization

Background

During the identification of potential candidates, computational prediction of drug-target interactions (DTIs) is important to subsequent expensive validation in wet-lab. DTI screening considers four scenarios, depending on whether the drug is an existing or a new drug and whether the target is an existing or a new target. However, existing approaches have the following limitations. First, only a few of them can address the most difficult scenario (i.e., predicting interactions between new drugs and new targets). More importantly, none of the existing approaches could provide the explicit information for understanding the mechanism of forming interactions, such as the drug-target feature pairs contributing to the interactions.

Results

In this paper, we propose a Triple Matrix Factorization-based model (TMF) to tackle these problems. Compared with former state-of-the-art predictive methods, TMF demonstrates its significant superiority by assessing the predictions on four benchmark datasets over four kinds of screening scenarios. Also, it exhibits its outperformance by validating predicted novel interactions. More importantly, by using PubChem fingerprints of chemical structures as drug features and occurring frequencies of amino acid trimer as protein features, TMF shows its ability to find out the features determining interactions, including dominant feature pairs, frequently occurring substructures, and conserved triplet of amino acids.

Conclusions

Our TMF provides a unified framework of DTI prediction for all the screening scenarios. It also presents a new insight for the underlying mechanism of DTIs by indicating dominant features, which play important roles in the forming of DTI.