An Integrated In Silico Approach to Design Specific Inhibitors Targeting Human Poly(A)-Specific Ribonuclease

Poly(A)-specific ribonuclease (PARN) is an exoribonuclease/deadenylase that degrades 3′-end poly(A) tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN’s catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A) amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP-poly(A) inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential.     

Microbial ecology of fish species ongrowing in Greek sea farms and their watery environment

The present study focuses on the bacteriological profile of both watery ecosystem and fishes from different North and Central West Greek fish-farms ongrowing euryhaline fish species. The natural microflora of the fish and the water of their ongrowing units in selected farms were studied for a period of 20 months. The analyzed samples were mainly sea bream (Sparus aurata) 61.3% and sea bass (Dicentrarchus labrax) 24%. In most of the watery ecosystems coming from the different sampling areas, total and fecal coliforms as well as total and fecal streptococci were abundant in all water samples. Enterococcus, Escherichia coli and Pseudomonas were present at a level of 3 logs cfu/100 ml. The anaerobic Clostridium perfringens was found in vegetative (21.3%) and spore forms (13.3%). It is of interest to note that pathogens as Pasteurella piscicida and Vibrio anguillarum were isolated only in a small number of samples. Staphylococcus aureus was detected in 4% of the samples, other Staphylococcus sp. in 29.3%, E. coli in 30.7%, Salmonella sp. in 1.3%, Pseudomonas sp. in 13.3%, Clostridia lec(−) in 49.3%, Bacillus sp. in 38.7%, Vibrio sp. in 18.7%, Lactobacillus and Lactococcus sp. in 36% και 29.3% respectively. Vegetative forms of C. perfringens were detected in 22.7%.Although, our results showed no significant correlations between the sea water and fish microflora, more focus on this bipolar interacting system should be necessary in order to avoid any possible disturbance in the balance of the healthy farming ecosystem with the host organisms.     

Antibacterial activities of essential oils from eight Greek aromatic plants against clinical isolates of Staphylococcus aureus

Aromatic plants have been used widely to extend the shelf life of foods but at the same time research is undergoes for their properties as antibacterial agents in clinical use. Although there are promising results for the antimicrobial properties of various essential oils against environmental or food-isolated strains of Staphylococcus aureus, limited work has been done concerning these properties against clinical isolates of this pathogen. S. aureus is responsible for an increase number of nosocomial infections and at the same time exhibits increased resistance to synthetic agents.In this study, essential oils from eight aromatic plants common in Greece were isolated by hydrodistillation, analyzed by gas chromatography (GC) and GC/mass spectrometry (GC/MS) for their chemical components and tested for their antimicrobial activities against 24 clinical isolates of S. aureus. The methods used were disk diffusion and broth dilution in order to determine the Minimum Inhibitory Concentration (MIC).Our results showed that essential oils from Origanum vulgare and Origanum dictamnus were active against S. aureus when tested by disk diffusion, but exhibited increased MIC values (>256 mg/L) with the dilution method. In contrast, the reference strain NCTC 6571 showed to be extremely sensitive in most of the oils tested (MICs 0.25−32.0 mg/L) and resistant only to the essential oil from Ocimum basilicum. Therefore, there is no evidence of a potential clinical use for those essential oils and further research is needed in order to determine if they could substitute efficiently synthetic antibiotics or, perhaps be used in combination.     

Modulation of Poly(ADP-Ribose) Polymerase-1 (PARP-1)-Mediated Oxidative Cell Injury by Ring Finger Protein 146 (RNF146) in Cardiac Myocytes

Poly(ADP-ribose) polymerase-1 (PARP-1) activation is a hallmark of oxidative stress–induced cellular injury that can lead to energetic failure and necrotic cell death via depleting the cellular nicotinamide adenine dinucleotide (NAD⁺) and ATP pools. Pharmacological PARP-1 inhibition or genetic PARP-1 deficiency exert protective effects in multiple models of cardiomyocyte injury. However, the connection between nuclear PARP-1 activation and depletion of the cytoplasmic and mitochondrial energy pools is poorly understood. By using cultured rat cardiomyocytes, here we report that ring finger protein 146 (RNF146), a cytoplasmic E3-ubiquitin ligase, acts as a direct interactor of PARP-1. Overexpression of RNF146 exerts protection against oxidant-induced cell death, whereas PARP-1–mediated cellular injury is augmented after RNF146 silencing. RNF146 translocates to the nucleus upon PARP-1 activation, triggering the exit of PARP-1 from the nucleus, followed by rapid degradation of both proteins. PARP-1 and RNF146 degradation occurs in the early phase of myocardial ischemia-reperfusion injury; it precedes the induction of heat shock protein expression. Taken together, PARP-1 release from the nucleus and its rapid degradation represent newly identified steps of the necrotic cell death program induced by oxidative stress. These steps are controlled by the ubiquitin-proteasome pathway protein RNF146. The current results shed new light on the mechanism of necrotic cell death. RNF146 may represent a distinct target for experimental therapeutic intervention of oxidant-mediated cardiac injury.     

Neuronal Survival,Morphology and Outgrowth of Spiral Ganglion Neurons Using a Defined Growth Factor Combination

Objectives

The functionality of cochlear implants (CI) depends, among others, on the number and excitability of surviving spiral ganglion neurons (SGN). The spatial separation between the SGN, located in the bony axis of the inner ear, and the CI, which is inserted in the scala tympani, results in suboptimal performance of CI patients and may be decreased by attracting the SGN neurites towards the electrode contacts. Neurotrophic factors (NTFs) can support neuronal survival and neurite outgrowth.

Methods

Since brain-derived neurotrophic factor (BDNF) is well known for its neuroprotective effect and ciliary neurotrophic factor (CNTF) increases neurite outgrowth, we evaluated if the combination of BDNF and CNTF leads to an enhanced neuronal survival with extended neurite outgrowth. Both NTFs were added in effective high concentrations (BDNF 50ng/ml, CNTF 100ng/ml), alone and in combination, to cultured dissociated SGN of neonatal rats for 48 hours.

Results

The neuronal survival and neurite outgrowth were significantly higher in SGN treated with the combination of the two NTFs compared to treatment with each factor alone. Additionally, with respect to the morphology, the combination of BDNF and CNTF leads to a significantly higher number of bipolar neurons and a decreased number of neurons without neurites in culture.

Conclusion

The combination of BDNF and CNTF shows a great potential to increase the neuronal survival and the number of bipolar neurons in vitro and to regenerate retracted nerve fibers.     

Heat shock factor 1 in brain tumors: a link with transient receptor potential channels TRPV1 and TRPA1

Journal of Molecular Histology - Novel data report a “cross-talk” between Heat-Shock Factor 1 (HSF1) and the transient receptor potential vanilloid 1 cation channel (TRPV1) located in...     

About the action of metabolites of plant growth-promoting rhizobacteria Bacillus subtilis on plant salt tolerance (I)

To find out the mode of plant tolerance enhancement against salinity by plant growth-promoting rhizobacteria Bacillus subtilis, metabolites of strains FZB24 and FZB41 were studied in a test system with tomatoes under the influence of high salinity. The culture filtrate (CF) from the fermentative transitional phase, containing the whole range of produced metabolites by B. subtilis, showed to a certain extent tolerance-increasing action at dilution of 0.1% in the test plants with the parameters length, fresh mass and dry mass of shoots and roots as well as leaf area after 7-day treatment and subsequent plant cultivation under high salt stress. Afterwards, the CF was fractionated with adsorber resin and high performance liquid chromatography, and these fractions, as well as fractions from a CF after 19-h fermentation, were also tested with axenic-cultivated tomato seedlings. Fractions with different proteins and peptides, produced by B. subtilis, showed partly activities depending on concentration with regard to plant growth stimulation, including tolerance enhancement against salt stress. Subsequently, also an extract from B. subtilis culture with special concentrated peptides was examined in the axenic plant test system and showed similar activity depending on concentration. The observed effect of the bacterial metabolites is discussed as one part of the mechanism for plant growth stimulation and at the same time salt tolerance, increasing action of the rhizobacterium by its root colonization and interaction with the plant metabolism.     

TPPII promotes genetic instability by allowing the escape from apoptosis of cells with activated mitotic checkpoints

Overexpression of TPPII correlates with accelerated growth and the appearance of centrosome and chromosome aberrations, suggesting that the activity of this enzyme may be critical for the induction and/or maintenance of genetic instability in malignant cells. We now find that the length of mitosis and of the entire cell cycle is significantly reduced in TPPII overexpressing HEK293 cells compared to untransfected and control transfected cells. Functional TPPII knockdown by shRNA interference caused a significant slowdown in cell growth and the accumulation of cells that delayed or failed to complete mitosis. TPPII overexpressing cells evade mitotic arrest induced by spindle poisons and display high levels of polyploidy despite the constitutively high expression of major components of the spindle checkpoint. TPPII overexpression correlated with upregulation of IAPs and with resistance to mitochondria dependent apoptosis induced by p53 stabilization. Thus, TPPII appears to promote malignant cell growth by allowing exit from mitosis and the survival of cells with severe mitotic spindle damage.